1PCR

STRUCTURE OF THE PHOTOSYNTHETIC REACTION CENTRE FROM RHODOBACTER SPHAEROIDES AT 2.65 ANGSTROMS RESOLUTION: COFACTORS AND PROTEIN-COFACTOR INTERACTIONS

PDB DOI: https://doi.org/10.2210/pdb1PCR/pdb

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

Deposited: 1994-11-10 Released: 1995-02-07
Deposition Author(s): Ermler, U., Fritzsch, G., Michel, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Work: 0.186
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7F0L

Literature

Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 A resolution: cofactors and protein-cofactor interactions.

Ermler, U., Fritzsch, G., Buchanan, S.K., Michel, H.

(1994) Structure 2: 925-936

PubMed: 7866744 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(94)00094-8
Primary Citation of Related Structures:
1PCR

PubMed Abstract:
Photosynthetic reaction centres (RCs) catalyze light-driven electron, transport across photosynthetic membranes. The photosynthetic bacterium Rhodobacter, sphaeroides is often used for studies of RCs, and three groups have determined the structure of its reaction centre. There are discrepancies between these structures, however, and to resolve these we have determined the structure to higher resolution than before, using a new crystal form.

Organizational Affiliation

Max-Planck-Institut für Biophysik, Frankfurt/Main, Germany.

Macromolecule Content

Total Structure Weight: 103.75 kDa
Atom Count: 7,311
Modelled Residue Count: 823
Deposited Residue Count: 848
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER	A [auth L]	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER	B [auth M]	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	C [auth H]	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain F [auth L] SDF format, chain N [auth M] SDF format, chain E [auth L] MOL2 format, chain D [auth L] MOL2 format, chain F [auth L] MOL2 format, chain N [auth M] MOL2 format, chain E [auth L]	D [auth L], E [auth L], F [auth L], N [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain N [auth M]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain O [auth M] MOL2 format, chain G [auth L] MOL2 format, chain O [auth M]	G [auth L], O [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain G [auth L] Focus chain O [auth M]
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain P [auth M] MOL2 format, chain H [auth L] MOL2 format, chain P [auth M]	H [auth L], P [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain H [auth L] Focus chain P [auth M]
SPO Query on SPO Download Ideal Coordinates CCD File SDF format, chain Q [auth M] MOL2 format, chain Q [auth M]	Q [auth M]	SPHEROIDENE C₄₁ H₆₀ O FJOCMTHZSURUFA-KXCOHNEYSA-N		Interactions Focus chain Q [auth M]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain S [auth M] SDF format, chain U [auth M] SDF format, chain V [auth M] SDF format, chain W [auth M] SDF format, chain I [auth L] SDF format, chain R [auth M] SDF format, chain T [auth M] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain S [auth M] MOL2 format, chain U [auth M] MOL2 format, chain V [auth M] MOL2 format, chain W [auth M] MOL2 format, chain I [auth L] MOL2 format, chain R [auth M] MOL2 format, chain T [auth M]	I [auth L] J [auth L] K [auth L] R [auth M] S [auth M] I [auth L], J [auth L], K [auth L], R [auth M], S [auth M], T [auth M], U [auth M], V [auth M], W [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain V [auth M] Focus chain W [auth M]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M MOL2 format, chain M	M	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain L [auth M] MOL2 format, chain L [auth M]	L [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain L [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Work: 0.186
R-Value Observed: 0.186
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.3	α = 90
b = 141.3	β = 90
c = 187.2	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1995-02-07

Deposition Author(s):

Ermler, U.

Fritzsch, G.

Michel, H.

Revision History (Full details and data files)

Version 1.0: 1995-02-07
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: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Other