4IXQ

RT fs X-ray diffraction of Photosystem II, dark state

• PDB DOI: https://doi.org/10.2210/pdb4IXQ/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Thermosynechococcus vestitus BP-1
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2013-01-27 Released: 2013-02-20 
• Deposition Author(s): Kern, J., Alonso-Mori, R., Tran, R., Hattne, J., Gildea, R.J., Echols, N., Gloeckner, C., Hellmich, J., Laksmono, H., Sierra, R.G., Lassalle-Kaiser, B., Koroidov, S., Lampe, A., Han, G., Gul, S., DiFiore, D., Milathianaki, D., Fry, A.R., Miahnahri, A., Schafer, D.W., Messerschmidt, M., Seibert, M.M., Koglin, J.E., Sokaras, D., Weng, T.-C., Sellberg, J., Latimer, M.J., Grosse-Kunstleve, R.W., Zwart, P.H., White, W.E., Glatzel, P., Adams, P.D., Bogan, M.J., Williams, G.J., Boutet, S., Messinger, J., Zouni, A., Sauter, N.K., Yachandra, V.K., Bergmann, U., Yano, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.70 Å
• R-Value Free: 
  0.314 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.279 (Depositor) 

Starting Model: experimental

Literature

Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Kern, J., Alonso-Mori, R., Tran, R., Hattne, J., Gildea, R.J., Echols, N., Glockner, C., Hellmich, J., Laksmono, H., Sierra, R.G., Lassalle-Kaiser, B., Koroidov, S., Lampe, A., Han, G., Gul, S., Difiore, D., Milathianaki, D., Fry, A.R., Miahnahri, A., Schafer, D.W., Messerschmidt, M., Seibert, M.M., Koglin, J.E., Sokaras, D., Weng, T.C., Sellberg, J., Latimer, M.J., Grosse-Kunstleve, R.W., Zwart, P.H., White, W.E., Glatzel, P., Adams, P.D., Bogan, M.J., Williams, G.J., Boutet, S., Messinger, J., Zouni, A., Sauter, N.K., Yachandra, V.K., Bergmann, U., Yano, J.

(2013) Science 340: 491-495

• PubMed: 23413188 
• DOI: https://doi.org/10.1126/science.1234273
• Primary Citation of Related Structures:  
  4IXQ, 4IXR


• PubMed Abstract: 
  

  Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.

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Organizational Affiliation: 

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 40-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 40-mer - A12B4C2D2E2F2G2H2I2J2K2L2M2N2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 765.69 kDa 
• Atom Count: 50,232 
• Modelled Residue Count: 5,270 
• Deposited Residue Count: 5,706 
• Unique protein chains: 20

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem Q(B) protein 1	A, U [auth a]	360	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A444  Go to UniProtKB:  P0A444

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II core light harvesting protein	B, V [auth b]	510	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIQ1  Go to UniProtKB:  Q8DIQ1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II CP43 protein	C, W [auth c]	461	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIF8  Go to UniProtKB:  Q8DIF8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II D2 protein	D, X [auth d]	352	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 1.10.3.9 Membrane Entity: Yes
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8CM25  Go to UniProtKB:  Q8CM25

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit alpha	E, Y [auth e]	84	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIP0  Go to UniProtKB:  Q8DIP0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b559 subunit beta	F, Z [auth f]	45	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIN9  Go to UniProtKB:  Q8DIN9

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein H	AA [auth h], G [auth H]	66	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJ43  Go to UniProtKB:  Q8DJ43

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein I	BA [auth i], H [auth I]	38	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJZ6  Go to UniProtKB:  Q8DJZ6

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein J	CA [auth j], I [auth J]	40	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P59087  Go to UniProtKB:  P59087

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein K	DA [auth k], J [auth K]	46	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1K9  Go to UniProtKB:  Q9F1K9

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein L	EA [auth l], K [auth L]	37	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIN8  Go to UniProtKB:  Q8DIN8

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein M	FA [auth m], L [auth M]	36	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DHA7  Go to UniProtKB:  Q8DHA7

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II manganese-stabilizing polypeptide	GA [auth o], M [auth O]	272	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A431  Go to UniProtKB:  P0A431

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein T	HA [auth t], N [auth T]	32	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIQ0  Go to UniProtKB:  Q8DIQ0

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II 12 kDa extrinsic protein	IA [auth u], O [auth U]	134	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1L5  Go to UniProtKB:  Q9F1L5

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-550	JA [auth v], P [auth V]	163	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A386  Go to UniProtKB:  P0A386

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein ycf12	KA [auth g], Q [auth y]	46	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DJI1  Go to UniProtKB:  Q8DJI1

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center X protein	LA [auth x], R [auth X]	41	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q9F1R6  Go to UniProtKB:  Q9F1R6

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Z	MA [auth z], S [auth Z]	62	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DHJ2  Go to UniProtKB:  Q8DHJ2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem II reaction center protein Y	NA [auth G], T [auth Y]	28	Thermosynechococcus vestitus BP-1	Mutation(s): 0

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	AC [auth B], FC [auth B], LD [auth D], NG [auth c], OG [auth c], PG [auth c], SE [auth a], SF [auth b], XC [auth C], YA [auth A], YC [auth C], YE [auth b], YG [auth d], ZC [auth C]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	AF [auth b], AG [auth c], BF [auth b], BG [auth c], CD [auth D], CF [auth b], CG [auth c], DF [auth b], DG [auth c], ED [auth D], EF [auth b], EG [auth c], FF [auth b], FG [auth c], GB [auth B], GF [auth b], GG [auth c], HB [auth B], HF [auth b], HG [auth c], IB [auth B], IC [auth C], IF [auth b], IG [auth c], JB [auth B], JC [auth C], JE [auth a], JF [auth b], JG [auth c], KB [auth B], KC [auth C], KE [auth a], KF [auth b], LB [auth B], LC [auth C], LE [auth a], LF [auth b], MB [auth B], MC [auth C], MF [auth b], NB [auth B], NC [auth C], NF [auth b], OB [auth B], OC [auth C], OE [auth a], OF [auth b], PB [auth B], PC [auth C], PF [auth b], QA [auth A], QB [auth B], QC [auth C], RA [auth A], RB [auth B], RC [auth C], SA [auth A], SB [auth B], SC [auth C], SG [auth d], TB [auth B], TC [auth C], TG [auth d], UA [auth A], UB [auth B], UC [auth C], VB [auth B], XF [auth c], YF [auth c], ZF [auth c]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO	DD [auth D], ME [auth a], NE [auth a], TA [auth A]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD	AB [auth A], DH [auth f], EB [auth A], EC [auth B], GE [auth a], KD [auth D], PD [auth F], UE [auth a], XE [auth b], XG [auth d]	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL C41 H78 O12 S RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG	AD [auth C], AH [auth e], BB [auth A], BC [auth B], BD [auth C], EH [auth i], FB [auth A], HD [auth D], HE [auth a], ID [auth D], JD [auth D], KH [auth k], ND [auth E], QG [auth c], RD [auth I], TF [auth b], UF [auth b], VE [auth a], VG [auth d], WG [auth d], XD [auth M], YD [auth M]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
PL9	FD [auth D], GH [auth j], PE [auth a], TD [auth J], UG [auth d], VA [auth A]	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE C53 H80 O2 FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG	CB [auth A], TE [auth a], WE [auth a], ZA [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM	BH [auth f], EE [auth V], NH [auth v], OD [auth F]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BCR	CE [auth T], CH [auth f], DE [auth T], FE [auth Z], GD [auth D], HH [auth j], JH [auth k], KG [auth c], LG [auth c], MG [auth c], OH [auth x], QD [auth H], QF [auth b], RE [auth a], RF [auth b], UD [auth J], VC [auth C], WB [auth B], WC [auth C], WD [auth K], XA [auth A], XB [auth B], YB [auth B], ZB [auth B]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
LMT	BE [auth T], CC [auth B], DC [auth B], FH [auth i], GC [auth B], HC [auth B], LH [auth m], MD [auth D], PH [auth x], SD [auth I], VF [auth b], WF [auth b], ZD [auth M], ZE [auth b]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEC	QE [auth a], WA [auth A]	OXYGEN EVOLVING SYSTEM Ca Mn4 O4 UFRGXNUNWYSFQE-UHFFFAOYSA-N
BCT	PA [auth A], RG [auth d]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2	IE [auth a], OA [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CA	AE [auth O], IH [auth k], MH [auth o], VD [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	DB [auth A], ZG [auth d]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.70 Å
• R-Value Free:  0.314 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.279 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.864	α = 90
b = 227.511	β = 90
c = 307.219	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
cctbx.xfel	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Kern, J., Alonso-Mori, R., Tran, R., Hattne, J., Gildea, R.J., Echols, N., Gloeckner, C., Hellmich, J., Laksmono, H., Sierra, R.G., Lassalle-Kaiser, B., Koroidov, S., Lampe, A., Han, G., Gul, S., DiFiore, D., Milathianaki, D., Fry, A.R., Miahnahri, A., Schafer, D.W., Messerschmidt, M., Seibert, M.M., Koglin, J.E., Sokaras, D., Weng, T.-C., Sellberg, J., Latimer, M.J., Grosse-Kunstleve, R.W., Zwart, P.H., White, W.E., Glatzel, P., Adams, P.D., Bogan, M.J., Williams, G.J., Boutet, S., Messinger, J., Zouni, A., Sauter, N.K., Yachandra, V.K., Bergmann, U., Yano, J.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2013-02-27
  Changes: Database references
• Version 1.2: 2013-05-08
  Changes: Database references
• Version 2.0: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
• Version 2.1: 2024-10-30
  Changes: Data collection, Structure summary