1AIJ

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE

PDB DOI: https://doi.org/10.2210/pdb1AIJ/pdb

Classification: PHOTOSYNTHETIC REACTION CENTER
Organism(s): Cereibacter sphaeroides
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 1997-04-18 Released: 1997-10-22
Deposition Author(s): Stowell, M.H.B., Mcphillips, T.M., Soltis, S.M., Rees, D.C., Abresch, E., Feher, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.270
R-Value Work: 0.216
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

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

Literature

Light-induced structural changes in photosynthetic reaction center: implications for mechanism of electron-proton transfer.

Stowell, M.H., McPhillips, T.M., Rees, D.C., Soltis, S.M., Abresch, E., Feher, G.

(1997) Science 276: 812-816

PubMed: 9115209 Search on PubMed
DOI: https://doi.org/10.1126/science.276.5313.812
Primary Citation of Related Structures:
1AIG, 1AIJ

PubMed Abstract:
High resolution x-ray diffraction data from crystals of the Rhodobacter sphaeroides photosynthetic reaction center (RC) have been collected at cryogenic temperature in the dark and under illumination, and the structures were refined at 2.2 and 2.6 angstrom resolution, respectively. In the charge-separated D+QAQB- state (where D is the primary electron donor (a bacteriochlorophyll dimer), and QA and QB are the primary and secondary quinone acceptors, respectively), QB- is located approximately 5 angstroms from the QB position in the charge-neutral (DQAQB) state, and has undergone a 180 degrees propeller twist around the isoprene chain. A model based on the difference between the two structures is proposed to explain the observed kinetics of electron transfer from QA-QB to QAQB- and the relative binding affinities of the different ubiquinone species in the QB pocket. In addition, several water channels (putative proton pathways) leading from the QB pocket to the surface of the RC were delineated, one of which leads directly to the membrane surface.

Organizational Affiliation

Division of Chemistry and Chemical Engineering, 147-75CH, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecule Content

Total Structure Weight: 203.1 kDa
Atom Count: 14,393
Modelled Residue Count: 1,654
Deposited Residue Count: 1,696
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)	A [auth L], D [auth R]	281	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides) Explore P0C0Y8 Go to UniProtKB: P0C0Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)	B [auth M], E [auth S]	307	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides) Explore P0C0Y9 Go to UniProtKB: P0C0Y9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)	C [auth H], F [auth T]	260	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7 Go to UniProtKB: P0C0Y7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain M SDF format, chain N [auth M] SDF format, chain T [auth R] SDF format, chain U [auth R] SDF format, chain Y [auth S] SDF format, chain Z [auth S] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain M MOL2 format, chain N [auth M] MOL2 format, chain T [auth R] MOL2 format, chain U [auth R] MOL2 format, chain Y [auth S] MOL2 format, chain Z [auth S]	G [auth L] H [auth L] M N [auth M] T [auth R] G [auth L], H [auth L], M, N [auth M], T [auth R], U [auth R], Y [auth S], Z [auth S]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain G [auth L] Focus chain H [auth L] Focus chain M Focus chain N [auth M] Focus chain T [auth R] Focus chain U [auth R] Focus chain Y [auth S] Focus chain Z [auth S]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain AA [auth S] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain V [auth R] MOL2 format, chain AA [auth S] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain V [auth R]	AA [auth S], I [auth L], J [auth L], V [auth R]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain AA [auth S] Focus chain I [auth L] Focus chain J [auth L] Focus chain V [auth R]
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain BA [auth S] SDF format, chain K [auth L] SDF format, chain O [auth M] SDF format, chain W [auth R] MOL2 format, chain BA [auth S] MOL2 format, chain K [auth L] MOL2 format, chain O [auth M] MOL2 format, chain W [auth R]	BA [auth S], K [auth L], O [auth M], W [auth R]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain BA [auth S] Focus chain K [auth L] Focus chain O [auth M] Focus chain W [auth R]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain P [auth M] SDF format, chain Q [auth M] SDF format, chain R [auth M] SDF format, chain S [auth M] MOL2 format, chain P [auth M] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M]	P [auth M], Q [auth M], R [auth M], S [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain P [auth M] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth M]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain L [auth M] SDF format, chain X [auth S] MOL2 format, chain L [auth M] MOL2 format, chain X [auth S]	L [auth M], X [auth S]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain L [auth M] Focus chain X [auth S]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.270
R-Value Work: 0.216
R-Value Observed: 0.216
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.08	α = 90
b = 140.08	β = 90
c = 271.63	γ = 90

Software Package:

Software Name	Purpose
MERLOT	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1997-10-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1997-10-22
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2019-11-20
Changes: Advisory, Database references, Derived calculations
Version 1.4: 2024-02-07
Changes: Advisory, Data collection, Database references, Derived calculations