3A0B | pdb_00003a0b

Crystal structure of Br-substituted Photosystem II complex

PDB DOI: https://doi.org/10.2210/pdb3A0B/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Thermostichus vulcanus
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2009-03-16 Released: 2009-05-19
Deposition Author(s): Kawakami, K., Umena, Y., Kamiya, N., Shen, J.-R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free:
0.358 (Depositor), 0.286 (DCC)
R-Value Work:
0.302 (Depositor), 0.286 (DCC)
R-Value Observed:
0.302 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography

Kawakami, K., Umena, Y., Kamiya, N., Shen, J.-R.

(2009) Proc Natl Acad Sci U S A 106: 8567-8572

PubMed: 19433803 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0812797106
Primary Citation Related Structures:
3A0B, 3A0H

PubMed Abstract:
The chloride ion, Cl(-), is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn(4)Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl(-) with a bromide ion (Br(-)) or an iodide ion (I(-)) in PSII and analyzed the crystal structures of PSII with Br(-) and I(-) substitutions. Substitution of Cl(-) with Br(-) did not inhibit oxygen evolution, whereas substitution of Cl(-) with I(-) completely inhibited oxygen evolution, indicating the efficient replacement of Cl(-) by I(-). PSII with Br(-) and I(-) substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn(4)Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn(4)Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl(-) anions are required to maintain the coordination structure of the Mn(4)Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.

Organizational Affiliation

Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University, Okayama 700-8530, Japan.

Macromolecule Content

Total Structure Weight: 683.97 kDa
Atom Count: 47,988
Modeled Residue Count: 5,242
Deposited Residue Count: 5,298
Unique protein chains: 20

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem Q(B) protein	A, U [auth a]	344	Thermostichus vulcanus	Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P51765 (Thermostichus vulcanus) Explore P51765 Go to UniProtKB: P51765
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51765
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II core light harvesting protein	B, V [auth b]	488	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus) Explore D0VWR1 Go to UniProtKB: D0VWR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWR1
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 protein	C, W [auth c]	447	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR7 (Thermostichus vulcanus) Explore D0VWR7 Go to UniProtKB: D0VWR7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWR7
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D, X [auth d]	340	Thermostichus vulcanus	Mutation(s): 0 EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus) Explore D0VWR8 Go to UniProtKB: D0VWR8
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWR8
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E, Y [auth e]	83	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12238 (Thermostichus vulcanus) Explore P12238 Go to UniProtKB: P12238
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12238
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F, Z [auth f]	44	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12239 (Thermostichus vulcanus) Explore P12239 Go to UniProtKB: P12239
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12239
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	AA [auth h], G [auth H]	64	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P19052 (Thermostichus vulcanus) Explore P19052 Go to UniProtKB: P19052
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19052
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	BA [auth i], H [auth I]	35	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12240 (Thermostichus vulcanus) Explore P12240 Go to UniProtKB: P12240
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12240
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	CA [auth j], I [auth J]	40	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus) Explore Q7DGD4 Go to UniProtKB: Q7DGD4
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7DGD4
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	DA [auth k], J [auth K]	36	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P19054 (Thermostichus vulcanus) Explore P19054 Go to UniProtKB: P19054
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19054
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	EA [auth l], K [auth L]	37	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12241 (Thermostichus vulcanus) Explore P12241 Go to UniProtKB: P12241
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12241
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	FA [auth m], L [auth M]	36	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12312 (Thermostichus vulcanus) Explore P12312 Go to UniProtKB: P12312
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12312
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II manganese-stabilizing polypeptide	GA [auth o], M [auth O]	242	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR2 (Thermostichus vulcanus) Explore D0VWR2 Go to UniProtKB: D0VWR2
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UniProt Group	D0VWR2
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	HA [auth t], N [auth T]	30	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P12313 (Thermostichus vulcanus) Explore P12313 Go to UniProtKB: P12313
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12313
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 12 kDa extrinsic protein	IA [auth u], O [auth U]	98	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P56152 (Thermostichus vulcanus) Explore P56152 Go to UniProtKB: P56152
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56152
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	JA [auth v], P [auth V]	137	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A387 (Thermostichus vulcanus) Explore P0A387 Go to UniProtKB: P0A387
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UniProt Group	P0A387
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein X	KA [auth x], Q [auth X]	34	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus) Explore D0VWR4 Go to UniProtKB: D0VWR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWR4
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein ycf12	LA [auth y], R [auth Y]	28	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus) Explore D0VWR3 Go to UniProtKB: D0VWR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWR3
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Y	MA [auth n], S [auth N]	24	Thermostichus vulcanus	Mutation(s): 0

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	NA [auth z], T [auth Z]	62	Thermostichus vulcanus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus) Explore D0VWR5 Go to UniProtKB: D0VWR5
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWR5
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Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD Query on DGD Download:Ideal Coordinates CCD File SDF format, chain HC [auth C] SDF format, chain IC [auth C] SDF format, chain IF [auth h] SDF format, chain JC [auth C] SDF format, chain UE [auth c] SDF format, chain VE [auth c] SDF format, chain TE [auth c] SDF format, chain TC [auth H] MOL2 format, chain HC [auth C] MOL2 format, chain IC [auth C] MOL2 format, chain IF [auth h] MOL2 format, chain JC [auth C] MOL2 format, chain UE [auth c] MOL2 format, chain VE [auth c] MOL2 format, chain TE [auth c] MOL2 format, chain TC [auth H] mmCIF format, chain HC [auth C] mmCIF format, chain IC [auth C] mmCIF format, chain IF [auth h] mmCIF format, chain JC [auth C] mmCIF format, chain UE [auth c] mmCIF format, chain VE [auth c] mmCIF format, chain TE [auth c] mmCIF format, chain TC [auth H]	HC [auth C] IC [auth C] IF [auth h] JC [auth C] TC [auth H] HC [auth C], IC [auth C], IF [auth h], JC [auth C], TC [auth H], TE [auth c], UE [auth c], VE [auth c]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain HC [auth C] Focus chain IC [auth C] Focus chain IF [auth h] Focus chain JC [auth C] Focus chain TC [auth H] Focus chain TE [auth c] Focus chain UE [auth c] Focus chain VE [auth c] Interactions & Density Focus chain HC [auth C] Focus chain IC [auth C] Focus chain IF [auth h] Focus chain JC [auth C] Focus chain TC [auth H] Focus chain TE [auth c] Focus chain UE [auth c] Focus chain VE [auth c]
CLA Query on CLA Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain AC [auth C] SDF format, chain AE [auth b] SDF format, chain BB [auth B] SDF format, chain BC [auth C] SDF format, chain CB [auth B] SDF format, chain CC [auth C] SDF format, chain DB [auth B] SDF format, chain DC [auth C] SDF format, chain DD [auth a] SDF format, chain EB [auth B] SDF format, chain EC [auth C] SDF format, chain ED [auth a] SDF format, chain FB [auth B] SDF format, chain FC [auth C] SDF format, chain FD [auth a] SDF format, chain FE [auth c] SDF format, chain GB [auth B] SDF format, chain GE [auth c] SDF format, chain HE [auth c] SDF format, chain IB [auth B] SDF format, chain IE [auth c] SDF format, chain JB [auth B] SDF format, chain JE [auth c] SDF format, chain KB [auth B] SDF format, chain KC [auth D] SDF format, chain KE [auth c] SDF format, chain LB [auth B] SDF format, chain LC [auth D] SDF format, chain LD [auth b] SDF format, chain LE [auth c] SDF format, chain MB [auth B] SDF format, chain MC [auth D] SDF format, chain MD [auth b] SDF format, chain ME [auth c] SDF format, chain NB [auth B] SDF format, chain ND [auth b] SDF format, chain NE [auth c] SDF format, chain OB [auth B] SDF format, chain OE [auth c] SDF format, chain QA [auth A] SDF format, chain QE [auth c] SDF format, chain RA [auth A] SDF format, chain RC [auth H] SDF format, chain RD [auth b] SDF format, chain RE [auth c] SDF format, chain SA [auth A] SDF format, chain SD [auth b] SDF format, chain TB [auth C] SDF format, chain TD [auth b] SDF format, chain UB [auth C] SDF format, chain UD [auth b] SDF format, chain VB [auth C] SDF format, chain WD [auth b] SDF format, chain WE [auth d] SDF format, chain XB [auth C] SDF format, chain XD [auth b] SDF format, chain XE [auth d] SDF format, chain YB [auth C] SDF format, chain YD [auth b] SDF format, chain YE [auth d] SDF format, chain ZB [auth C] SDF format, chain ZD [auth b] SDF format, chain WB [auth C] SDF format, chain VD [auth b] SDF format, chain QD [auth b] SDF format, chain PE [auth c] SDF format, chain PD [auth b] SDF format, chain OD [auth b] SDF format, chain HB [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth C] MOL2 format, chain AE [auth b] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth C] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth C] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth C] MOL2 format, chain DD [auth a] MOL2 format, chain EB [auth B] MOL2 format, chain EC [auth C] MOL2 format, chain ED [auth a] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth C] MOL2 format, chain FD [auth a] MOL2 format, chain FE [auth c] MOL2 format, chain GB [auth B] MOL2 format, chain GE [auth c] MOL2 format, chain HE [auth c] MOL2 format, chain IB [auth B] MOL2 format, chain IE [auth c] MOL2 format, chain JB [auth B] MOL2 format, chain JE [auth c] MOL2 format, chain KB [auth B] MOL2 format, chain KC [auth D] MOL2 format, chain KE [auth c] MOL2 format, chain LB [auth B] MOL2 format, chain LC [auth D] MOL2 format, chain LD [auth b] MOL2 format, chain LE [auth c] MOL2 format, chain MB [auth B] MOL2 format, chain MC [auth D] MOL2 format, chain MD [auth b] MOL2 format, chain ME [auth c] MOL2 format, chain NB [auth B] MOL2 format, chain ND [auth b] MOL2 format, chain NE [auth c] MOL2 format, chain OB [auth B] MOL2 format, chain OE [auth c] MOL2 format, chain QA [auth A] MOL2 format, chain QE [auth c] MOL2 format, chain RA [auth A] MOL2 format, chain RC [auth H] MOL2 format, chain RD [auth b] MOL2 format, chain RE [auth c] MOL2 format, chain SA [auth A] MOL2 format, chain SD [auth b] MOL2 format, chain TB [auth C] MOL2 format, chain TD [auth b] MOL2 format, chain UB [auth C] MOL2 format, chain UD [auth b] MOL2 format, chain VB [auth C] MOL2 format, chain WD [auth b] MOL2 format, chain WE [auth d] MOL2 format, chain XB [auth C] MOL2 format, chain XD [auth b] MOL2 format, chain XE [auth d] MOL2 format, chain YB [auth C] MOL2 format, chain YD [auth b] MOL2 format, chain YE [auth d] MOL2 format, chain ZB [auth C] MOL2 format, chain ZD [auth b] MOL2 format, chain WB [auth C] MOL2 format, chain VD [auth b] MOL2 format, chain QD [auth b] MOL2 format, chain PE [auth c] MOL2 format, chain PD [auth b] MOL2 format, chain OD [auth b] MOL2 format, chain HB [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain AC [auth C] mmCIF format, chain AE [auth b] mmCIF format, chain BB [auth B] mmCIF format, chain BC [auth C] mmCIF format, chain CB [auth B] mmCIF format, chain CC [auth C] mmCIF format, chain DB [auth B] mmCIF format, chain DC [auth C] mmCIF format, chain DD [auth a] mmCIF format, chain EB [auth B] mmCIF format, chain EC [auth C] mmCIF format, chain ED [auth a] mmCIF format, chain FB [auth B] mmCIF format, chain FC [auth C] mmCIF format, chain FD [auth a] mmCIF format, chain FE [auth c] mmCIF format, chain GB [auth B] mmCIF format, chain GE [auth c] mmCIF format, chain HE [auth c] mmCIF format, chain IB [auth B] mmCIF format, chain IE [auth c] mmCIF format, chain JB [auth B] mmCIF format, chain JE [auth c] mmCIF format, chain KB [auth B] mmCIF format, chain KC [auth D] mmCIF format, chain KE [auth c] mmCIF format, chain LB [auth B] mmCIF format, chain LC [auth D] mmCIF format, chain LD [auth b] mmCIF format, chain LE [auth c] mmCIF format, chain MB [auth B] mmCIF format, chain MC [auth D] mmCIF format, chain MD [auth b] mmCIF format, chain ME [auth c] mmCIF format, chain NB [auth B] mmCIF format, chain ND [auth b] mmCIF format, chain NE [auth c] mmCIF format, chain OB [auth B] mmCIF format, chain OE [auth c] mmCIF format, chain QA [auth A] mmCIF format, chain QE [auth c] mmCIF format, chain RA [auth A] mmCIF format, chain RC [auth H] mmCIF format, chain RD [auth b] mmCIF format, chain RE [auth c] mmCIF format, chain SA [auth A] mmCIF format, chain SD [auth b] mmCIF format, chain TB [auth C] mmCIF format, chain TD [auth b] mmCIF format, chain UB [auth C] mmCIF format, chain UD [auth b] mmCIF format, chain VB [auth C] mmCIF format, chain WD [auth b] mmCIF format, chain WE [auth d] mmCIF format, chain XB [auth C] mmCIF format, chain XD [auth b] mmCIF format, chain XE [auth d] mmCIF format, chain YB [auth C] mmCIF format, chain YD [auth b] mmCIF format, chain YE [auth d] mmCIF format, chain ZB [auth C] mmCIF format, chain ZD [auth b] mmCIF format, chain WB [auth C] mmCIF format, chain VD [auth b] mmCIF format, chain QD [auth b] mmCIF format, chain PE [auth c] mmCIF format, chain PD [auth b] mmCIF format, chain OD [auth b] mmCIF format, chain HB [auth B]	AB [auth B] AC [auth C] AE [auth b] BB [auth B] BC [auth C] AB [auth B], AC [auth C], AE [auth b], BB [auth B], BC [auth C], CB [auth B], CC [auth C], DB [auth B], DC [auth C], DD [auth a], EB [auth B], EC [auth C], ED [auth a], FB [auth B], FC [auth C], FD [auth a], FE [auth c], GB [auth B], GE [auth c], HB [auth B], HE [auth c], IB [auth B], IE [auth c], JB [auth B], JE [auth c], KB [auth B], KC [auth D], KE [auth c], LB [auth B], LC [auth D], LD [auth b], LE [auth c], MB [auth B], MC [auth D], MD [auth b], ME [auth c], NB [auth B], ND [auth b], NE [auth c], OB [auth B], OD [auth b], OE [auth c], PD [auth b], PE [auth c], QA [auth A], QD [auth b], QE [auth c], RA [auth A], RC [auth H], RD [auth b], RE [auth c], SA [auth A], SD [auth b], TB [auth C], TD [auth b], UB [auth C], UD [auth b], VB [auth C], VD [auth b], WB [auth C], WD [auth b], WE [auth d], XB [auth C], XD [auth b], XE [auth d], YB [auth C], YD [auth b], YE [auth d], ZB [auth C], ZD [auth b]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AE [auth b] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain DD [auth a] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain ED [auth a] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain FD [auth a] Focus chain FE [auth c] Focus chain GB [auth B] Focus chain GE [auth c] Focus chain HB [auth B] Focus chain HE [auth c] Focus chain IB [auth B] Focus chain IE [auth c] Focus chain JB [auth B] Focus chain JE [auth c] Focus chain KB [auth B] Focus chain KC [auth D] Focus chain KE [auth c] Focus chain LB [auth B] Focus chain LC [auth D] Focus chain LD [auth b] Focus chain LE [auth c] Focus chain MB [auth B] Focus chain MC [auth D] Focus chain MD [auth b] Focus chain ME [auth c] Focus chain NB [auth B] Focus chain ND [auth b] Focus chain NE [auth c] Focus chain OB [auth B] Focus chain OD [auth b] Focus chain OE [auth c] Focus chain PD [auth b] Focus chain PE [auth c] Focus chain QA [auth A] Focus chain QD [auth b] Focus chain QE [auth c] Focus chain RA [auth A] Focus chain RC [auth H] Focus chain RD [auth b] Focus chain RE [auth c] Focus chain SA [auth A] Focus chain SD [auth b] Focus chain TB [auth C] Focus chain TD [auth b] Focus chain UB [auth C] Focus chain UD [auth b] Focus chain VB [auth C] Focus chain VD [auth b] Focus chain WB [auth C] Focus chain WD [auth b] Focus chain WE [auth d] Focus chain XB [auth C] Focus chain XD [auth b] Focus chain XE [auth d] Focus chain YB [auth C] Focus chain YD [auth b] Focus chain YE [auth d] Focus chain ZB [auth C] Focus chain ZD [auth b] Interactions & Density Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AE [auth b] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain DD [auth a] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain ED [auth a] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain FD [auth a] Focus chain FE [auth c] Focus chain GB [auth B] Focus chain GE [auth c] Focus chain HB [auth B] Focus chain HE [auth c] Focus chain IB [auth B] Focus chain IE [auth c] Focus chain JB [auth B] Focus chain JE [auth c] Focus chain KB [auth B] Focus chain KC [auth D] Focus chain KE [auth c] Focus chain LB [auth B] Focus chain LC [auth D] Focus chain LD [auth b] Focus chain LE [auth c] Focus chain MB [auth B] Focus chain MC [auth D] Focus chain MD [auth b] Focus chain ME [auth c] Focus chain NB [auth B] Focus chain ND [auth b] Focus chain NE [auth c] Focus chain OB [auth B] Focus chain OD [auth b] Focus chain OE [auth c] Focus chain PD [auth b] Focus chain PE [auth c] Focus chain QA [auth A] Focus chain QD [auth b] Focus chain QE [auth c] Focus chain RA [auth A] Focus chain RC [auth H] Focus chain RD [auth b] Focus chain RE [auth c] Focus chain SA [auth A] Focus chain SD [auth b] Focus chain TB [auth C] Focus chain TD [auth b] Focus chain UB [auth C] Focus chain UD [auth b] Focus chain VB [auth C] Focus chain VD [auth b] Focus chain WB [auth C] Focus chain WD [auth b] Focus chain WE [auth d] Focus chain XB [auth C] Focus chain XD [auth b] Focus chain XE [auth d] Focus chain YB [auth C] Focus chain YD [auth b] Focus chain YE [auth d] Focus chain ZB [auth C] Focus chain ZD [auth b]
PHO Query on PHO Download:Ideal Coordinates CCD File SDF format, chain GD [auth a] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain ZE [auth d] MOL2 format, chain GD [auth a] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain ZE [auth d] mmCIF format, chain GD [auth a] mmCIF format, chain TA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain ZE [auth d]	GD [auth a], TA [auth A], UA [auth A], ZE [auth d]	PHEOPHYTIN A C₅₅ H₇₄ N₄ O₅ CQIKWXUXPNUNDV-RCBXBCQGSA-N		Interactions Focus chain GD [auth a] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain ZE [auth d] Interactions & Density Focus chain GD [auth a] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain ZE [auth d]
LHG Query on LHG Download:Ideal Coordinates CCD File SDF format, chain JD [auth a] SDF format, chain XA [auth A] MOL2 format, chain JD [auth a] MOL2 format, chain XA [auth A] mmCIF format, chain JD [auth a] mmCIF format, chain XA [auth A]	JD [auth a], XA [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain JD [auth a] Focus chain XA [auth A] Interactions & Density Focus chain JD [auth a] Focus chain XA [auth A]
MGE Query on MGE Download:Ideal Coordinates CCD File SDF format, chain CF [auth d] SDF format, chain DF [auth d] SDF format, chain EE [auth b] SDF format, chain EF [auth d] SDF format, chain PC [auth D] SDF format, chain SB [auth B] SDF format, chain UC [auth J] SDF format, chain XC [auth L] MOL2 format, chain CF [auth d] MOL2 format, chain DF [auth d] MOL2 format, chain EE [auth b] MOL2 format, chain EF [auth d] MOL2 format, chain PC [auth D] MOL2 format, chain SB [auth B] MOL2 format, chain UC [auth J] MOL2 format, chain XC [auth L] mmCIF format, chain CF [auth d] mmCIF format, chain DF [auth d] mmCIF format, chain EE [auth b] mmCIF format, chain EF [auth d] mmCIF format, chain PC [auth D] mmCIF format, chain SB [auth B] mmCIF format, chain UC [auth J] mmCIF format, chain XC [auth L]	CF [auth d] DF [auth d] EE [auth b] EF [auth d] PC [auth D] CF [auth d], DF [auth d], EE [auth b], EF [auth d], PC [auth D], SB [auth B], UC [auth J], XC [auth L]	(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE C₃₈ H₇₂ O₁₀ FIJGNIAJTZSERN-DQQGJSMTSA-N		Interactions Focus chain CF [auth d] Focus chain DF [auth d] Focus chain EE [auth b] Focus chain EF [auth d] Focus chain PC [auth D] Focus chain SB [auth B] Focus chain UC [auth J] Focus chain XC [auth L] Interactions & Density Focus chain CF [auth d] Focus chain DF [auth d] Focus chain EE [auth b] Focus chain EF [auth d] Focus chain PC [auth D] Focus chain SB [auth B] Focus chain UC [auth J] Focus chain XC [auth L]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain GF [auth e] SDF format, chain MF [auth v] SDF format, chain QC [auth E] SDF format, chain ZC [auth V] MOL2 format, chain GF [auth e] MOL2 format, chain MF [auth v] MOL2 format, chain QC [auth E] MOL2 format, chain ZC [auth V] mmCIF format, chain GF [auth e] mmCIF format, chain MF [auth v] mmCIF format, chain QC [auth E] mmCIF format, chain ZC [auth V]	GF [auth e], MF [auth v], QC [auth E], ZC [auth V]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain GF [auth e] Focus chain MF [auth v] Focus chain QC [auth E] Focus chain ZC [auth V] Interactions & Density Focus chain GF [auth e] Focus chain MF [auth v] Focus chain QC [auth E] Focus chain ZC [auth V]
PQ9 Query on PQ9 Download:Ideal Coordinates CCD File SDF format, chain AF [auth d] SDF format, chain VA [auth A] SDF format, chain NC [auth D] SDF format, chain HD [auth a] MOL2 format, chain AF [auth d] MOL2 format, chain VA [auth A] MOL2 format, chain NC [auth D] MOL2 format, chain HD [auth a] mmCIF format, chain AF [auth d] mmCIF format, chain VA [auth A] mmCIF format, chain NC [auth D] mmCIF format, chain HD [auth a]	AF [auth d], HD [auth a], NC [auth D], VA [auth A]	5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE C₄₃ H₆₄ O₂ JXUCGUASMMLSBH-HOHOQCMASA-N		Interactions Focus chain AF [auth d] Focus chain HD [auth a] Focus chain NC [auth D] Focus chain VA [auth A] Interactions & Density Focus chain AF [auth d] Focus chain HD [auth a] Focus chain NC [auth D] Focus chain VA [auth A]
BCR Query on BCR Download:Ideal Coordinates CCD File SDF format, chain AD [auth Z] SDF format, chain BE [auth b] SDF format, chain BF [auth d] SDF format, chain CE [auth b] SDF format, chain DE [auth b] SDF format, chain GC [auth C] SDF format, chain JF [auth k] SDF format, chain KF [auth k] SDF format, chain LF [auth t] SDF format, chain NF [auth z] SDF format, chain OC [auth D] SDF format, chain PB [auth B] SDF format, chain QB [auth B] SDF format, chain RB [auth B] SDF format, chain SC [auth H] SDF format, chain SE [auth c] SDF format, chain VC [auth K] SDF format, chain WA [auth A] SDF format, chain WC [auth K] SDF format, chain YC [auth T] SDF format, chain ID [auth a] SDF format, chain HF [auth h] MOL2 format, chain AD [auth Z] MOL2 format, chain BE [auth b] MOL2 format, chain BF [auth d] MOL2 format, chain CE [auth b] MOL2 format, chain DE [auth b] MOL2 format, chain GC [auth C] MOL2 format, chain JF [auth k] MOL2 format, chain KF [auth k] MOL2 format, chain LF [auth t] MOL2 format, chain NF [auth z] MOL2 format, chain OC [auth D] MOL2 format, chain PB [auth B] MOL2 format, chain QB [auth B] MOL2 format, chain RB [auth B] MOL2 format, chain SC [auth H] MOL2 format, chain SE [auth c] MOL2 format, chain VC [auth K] MOL2 format, chain WA [auth A] MOL2 format, chain WC [auth K] MOL2 format, chain YC [auth T] MOL2 format, chain ID [auth a] MOL2 format, chain HF [auth h] mmCIF format, chain AD [auth Z] mmCIF format, chain BE [auth b] mmCIF format, chain BF [auth d] mmCIF format, chain CE [auth b] mmCIF format, chain DE [auth b] mmCIF format, chain GC [auth C] mmCIF format, chain JF [auth k] mmCIF format, chain KF [auth k] mmCIF format, chain LF [auth t] mmCIF format, chain NF [auth z] mmCIF format, chain OC [auth D] mmCIF format, chain PB [auth B] mmCIF format, chain QB [auth B] mmCIF format, chain RB [auth B] mmCIF format, chain SC [auth H] mmCIF format, chain SE [auth c] mmCIF format, chain VC [auth K] mmCIF format, chain WA [auth A] mmCIF format, chain WC [auth K] mmCIF format, chain YC [auth T] mmCIF format, chain ID [auth a] mmCIF format, chain HF [auth h]	AD [auth Z] BE [auth b] BF [auth d] CE [auth b] DE [auth b] AD [auth Z], BE [auth b], BF [auth d], CE [auth b], DE [auth b], GC [auth C], HF [auth h], ID [auth a], JF [auth k], KF [auth k], LF [auth t], NF [auth z], OC [auth D], PB [auth B], QB [auth B], RB [auth B], SC [auth H], SE [auth c], VC [auth K], WA [auth A], WC [auth K], YC [auth T]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain AD [auth Z] Focus chain BE [auth b] Focus chain BF [auth d] Focus chain CE [auth b] Focus chain DE [auth b] Focus chain GC [auth C] Focus chain HF [auth h] Focus chain ID [auth a] Focus chain JF [auth k] Focus chain KF [auth k] Focus chain LF [auth t] Focus chain NF [auth z] Focus chain OC [auth D] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SC [auth H] Focus chain SE [auth c] Focus chain VC [auth K] Focus chain WA [auth A] Focus chain WC [auth K] Focus chain YC [auth T] Interactions & Density Focus chain AD [auth Z] Focus chain BE [auth b] Focus chain BF [auth d] Focus chain CE [auth b] Focus chain DE [auth b] Focus chain GC [auth C] Focus chain HF [auth h] Focus chain ID [auth a] Focus chain JF [auth k] Focus chain KF [auth k] Focus chain LF [auth t] Focus chain NF [auth z] Focus chain OC [auth D] Focus chain PB [auth B] Focus chain QB [auth B] Focus chain RB [auth B] Focus chain SC [auth H] Focus chain SE [auth c] Focus chain VC [auth K] Focus chain WA [auth A] Focus chain WC [auth K] Focus chain YC [auth T]
OEC Query on OEC Download:Ideal Coordinates CCD File SDF format, chain BD [auth a] SDF format, chain OA [auth A] MOL2 format, chain BD [auth a] MOL2 format, chain OA [auth A] mmCIF format, chain BD [auth a] mmCIF format, chain OA [auth A]	BD [auth a], OA [auth A]	OXYGEN EVOLVING SYSTEM Ca Mn₄ O₄ UFRGXNUNWYSFQE-UHFFFAOYSA-N		Interactions Focus chain BD [auth a] Focus chain OA [auth A] Interactions & Density Focus chain BD [auth a] Focus chain OA [auth A]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain FF [auth d] SDF format, chain KD [auth a] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] MOL2 format, chain FF [auth d] MOL2 format, chain KD [auth a] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A] mmCIF format, chain FF [auth d] mmCIF format, chain KD [auth a] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth A]	FF [auth d], KD [auth a], YA [auth A], ZA [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain FF [auth d] Focus chain KD [auth a] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain FF [auth d] Focus chain KD [auth a] Focus chain YA [auth A] Focus chain ZA [auth A]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain CD [auth a] SDF format, chain PA [auth A] MOL2 format, chain CD [auth a] MOL2 format, chain PA [auth A] mmCIF format, chain CD [auth a] mmCIF format, chain PA [auth A]	CD [auth a], PA [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain CD [auth a] Focus chain PA [auth A] Interactions & Density Focus chain CD [auth a] Focus chain PA [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free: 0.358 (Depositor), 0.286 (DCC)
R-Value Work: 0.302 (Depositor), 0.286 (DCC)
R-Value Observed: 0.302 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.589	α = 90
b = 226.394	β = 90
c = 307.514	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-05-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-05-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
Version 2.1: 2024-10-23
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

3A0B | pdb_00003a0b

Crystal structure of Br-substituted Photosystem II complex

Literature

Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography

Biological Assembly 1

Macromolecules

Entity ID: 1

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