1PYH | pdb_00001pyh

Crystal structure of RC-LH1 core complex from Rhodopseudomonas palustris

PDB DOI: https://doi.org/10.2210/pdb1PYH/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Rhodopseudomonas palustris
Mutation(s): No

Deposited: 2003-07-08 Released: 2004-03-02
Deposition Author(s): Roszak, A.W., Howard, T.D., Southall, J., Gardiner, A.T., Law, C.J., Isaacs, N.W., Cogdell, R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.80 Å
R-Value Free:
0.491 (Depositor), 0.476 (DCC)
R-Value Work:
0.467 (Depositor), 0.455 (DCC)
R-Value Observed:
0.469 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris.

Roszak, A.W., Howard, T.D., Southall, J., Gardiner, A.T., Law, C.J., Isaacs, N.W., Cogdell, R.J.

(2003) Science 302: 1969-1972

PubMed: 14671305 Search on PubMed
DOI: https://doi.org/10.1126/science.1088892
Primary Citation Related Structures:
1PYH

PubMed Abstract:
The crystal structure at 4.8 angstrom resolution of the reaction center-light harvesting 1 (RC-LH1) core complex from Rhodopseudomonas palustris shows the reaction center surrounded by an oval LH1 complex that consists of 15 pairs of transmembrane helical alpha- and beta-apoproteins and their coordinated bacteriochlorophylls. Complete closure of the RC by the LH1 is prevented by a single transmembrane helix, out of register with the array of inner LH1 alpha-apoproteins. This break, located next to the binding site in the reaction center for the secondary electron acceptor ubiquinone (UQB), may provide a portal through which UQB can transfer electrons to cytochrome b/c1.

Organizational Affiliation

Department of Chemistry, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.

Macromolecule Content

Total Structure Weight: 177.26 kDa
Atom Count: 10,100
Modeled Residue Count: 1,690
Deposited Residue Count: 1,690
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	A	281	Rhodopseudomonas palustris	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	B	302	Rhodopseudomonas palustris	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	C	241	Rhodopseudomonas palustris	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-800/850, alpha chain	AA [auth 1] CA [auth 3] D EA [auth 5] F AA [auth 1], CA [auth 3], D, EA [auth 5], F, GA [auth 7], H, J, L, N, P, R, T, V, X, Z	26	Rhodopseudomonas palustris	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-800/850, beta chain	BA [auth 2] DA [auth 4] E FA [auth 6] G BA [auth 2], DA [auth 4], E, FA [auth 6], G, HA [auth 8], I, K, M, O, Q, S, U, W, Y	30	Rhodopseudomonas palustris	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL Query on BCL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth N] SDF format, chain YA [auth M] SDF format, chain XA [auth L] SDF format, chain WA [auth K] SDF format, chain VA [auth J] SDF format, chain UA [auth I] SDF format, chain TA [auth H] SDF format, chain SB [auth 8] SDF format, chain SA [auth G] SDF format, chain RB [auth 7] SDF format, chain RA [auth F] SDF format, chain QB [auth 6] SDF format, chain QA [auth E] SDF format, chain PB [auth 5] SDF format, chain PA [auth D] SDF format, chain OB [auth 3] SDF format, chain NB [auth 3] SDF format, chain NA [auth B] SDF format, chain MB [auth 2] SDF format, chain MA [auth B] SDF format, chain LB [auth 1] SDF format, chain KB [auth Y] SDF format, chain JB [auth Y] SDF format, chain JA [auth A] SDF format, chain IB [auth W] SDF format, chain IA [auth A] SDF format, chain HB [auth V] SDF format, chain GB [auth U] SDF format, chain FB [auth T] SDF format, chain EB [auth S] SDF format, chain DB [auth R] SDF format, chain CB [auth P] SDF format, chain BB [auth P] SDF format, chain AB [auth N] MOL2 format, chain ZA [auth N] MOL2 format, chain YA [auth M] MOL2 format, chain XA [auth L] MOL2 format, chain WA [auth K] MOL2 format, chain VA [auth J] MOL2 format, chain UA [auth I] MOL2 format, chain TA [auth H] MOL2 format, chain SB [auth 8] MOL2 format, chain SA [auth G] MOL2 format, chain RB [auth 7] MOL2 format, chain RA [auth F] MOL2 format, chain QB [auth 6] MOL2 format, chain QA [auth E] MOL2 format, chain PB [auth 5] MOL2 format, chain PA [auth D] MOL2 format, chain OB [auth 3] MOL2 format, chain NB [auth 3] MOL2 format, chain NA [auth B] MOL2 format, chain MB [auth 2] MOL2 format, chain MA [auth B] MOL2 format, chain LB [auth 1] MOL2 format, chain KB [auth Y] MOL2 format, chain JB [auth Y] MOL2 format, chain JA [auth A] MOL2 format, chain IB [auth W] MOL2 format, chain IA [auth A] MOL2 format, chain HB [auth V] MOL2 format, chain GB [auth U] MOL2 format, chain FB [auth T] MOL2 format, chain EB [auth S] MOL2 format, chain DB [auth R] MOL2 format, chain CB [auth P] MOL2 format, chain BB [auth P] MOL2 format, chain AB [auth N] mmCIF format, chain ZA [auth N] mmCIF format, chain YA [auth M] mmCIF format, chain XA [auth L] mmCIF format, chain WA [auth K] mmCIF format, chain VA [auth J] mmCIF format, chain UA [auth I] mmCIF format, chain TA [auth H] mmCIF format, chain SB [auth 8] mmCIF format, chain SA [auth G] mmCIF format, chain RB [auth 7] mmCIF format, chain RA [auth F] mmCIF format, chain QB [auth 6] mmCIF format, chain QA [auth E] mmCIF format, chain PB [auth 5] mmCIF format, chain PA [auth D] mmCIF format, chain OB [auth 3] mmCIF format, chain NB [auth 3] mmCIF format, chain NA [auth B] mmCIF format, chain MB [auth 2] mmCIF format, chain MA [auth B] mmCIF format, chain LB [auth 1] mmCIF format, chain KB [auth Y] mmCIF format, chain JB [auth Y] mmCIF format, chain JA [auth A] mmCIF format, chain IB [auth W] mmCIF format, chain IA [auth A] mmCIF format, chain HB [auth V] mmCIF format, chain GB [auth U] mmCIF format, chain FB [auth T] mmCIF format, chain EB [auth S] mmCIF format, chain DB [auth R] mmCIF format, chain CB [auth P] mmCIF format, chain BB [auth P] mmCIF format, chain AB [auth N]	AB [auth N] BB [auth P] CB [auth P] DB [auth R] EB [auth S] AB [auth N], BB [auth P], CB [auth P], DB [auth R], EB [auth S], FB [auth T], GB [auth U], HB [auth V], IA [auth A], IB [auth W], JA [auth A], JB [auth Y], KB [auth Y], LB [auth 1], MA [auth B], MB [auth 2], NA [auth B], NB [auth 3], OB [auth 3], PA [auth D], PB [auth 5], QA [auth E], QB [auth 6], RA [auth F], RB [auth 7], SA [auth G], SB [auth 8], TA [auth H], UA [auth I], VA [auth J], WA [auth K], XA [auth L], YA [auth M], ZA [auth N]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AB [auth N] Focus chain BB [auth P] Focus chain CB [auth P] Focus chain DB [auth R] Focus chain EB [auth S] Focus chain FB [auth T] Focus chain GB [auth U] Focus chain HB [auth V] Focus chain IA [auth A] Focus chain IB [auth W] Focus chain JA [auth A] Focus chain JB [auth Y] Focus chain KB [auth Y] Focus chain LB [auth 1] Focus chain MA [auth B] Focus chain MB [auth 2] Focus chain NA [auth B] Focus chain NB [auth 3] Focus chain OB [auth 3] Focus chain PA [auth D] Focus chain PB [auth 5] Focus chain QA [auth E] Focus chain QB [auth 6] Focus chain RA [auth F] Focus chain RB [auth 7] Focus chain SA [auth G] Focus chain SB [auth 8] Focus chain TA [auth H] Focus chain UA [auth I] Focus chain VA [auth J] Focus chain WA [auth K] Focus chain XA [auth L] Focus chain YA [auth M] Focus chain ZA [auth N] Interactions & Density Focus chain AB [auth N] Focus chain BB [auth P] Focus chain CB [auth P] Focus chain DB [auth R] Focus chain EB [auth S] Focus chain FB [auth T] Focus chain GB [auth U] Focus chain HB [auth V] Focus chain IA [auth A] Focus chain IB [auth W] Focus chain JA [auth A] Focus chain JB [auth Y] Focus chain KB [auth Y] Focus chain LB [auth 1] Focus chain MA [auth B] Focus chain MB [auth 2] Focus chain NA [auth B] Focus chain NB [auth 3] Focus chain OB [auth 3] Focus chain PA [auth D] Focus chain PB [auth 5] Focus chain QA [auth E] Focus chain QB [auth 6] Focus chain RA [auth F] Focus chain RB [auth 7] Focus chain SA [auth G] Focus chain SB [auth 8] Focus chain TA [auth H] Focus chain UA [auth I] Focus chain VA [auth J] Focus chain WA [auth K] Focus chain XA [auth L] Focus chain YA [auth M] Focus chain ZA [auth N]
BPH Query on BPH Download:Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain KA [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain KA [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain KA [auth A]	KA [auth A], OA [auth B]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain KA [auth A] Focus chain OA [auth B] Interactions & Density Focus chain KA [auth A] Focus chain OA [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] MOL2 format, chain LA [auth B] mmCIF format, chain LA [auth B]	LA [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Interactions & Density Focus chain LA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.80 Å
R-Value Free: 0.491 (Depositor), 0.476 (DCC)
R-Value Work: 0.467 (Depositor), 0.455 (DCC)
R-Value Observed: 0.469 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.037	α = 69.32
b = 119.024	β = 72.69
c = 130.432	γ = 66.52

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-03-02
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description