1PCR

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


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

  • 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. The new structure provides a more detailed description of the Rb. sphaeroides RC, and allows us to compare it with the structure of the RC from Rhodopseudomonas viridis. We find no evidence to support most of the published differences in cofactor binding between the RCs from Rps. viridis and Rb. sphaeroides. Generally, the mode of cofactor binding is conserved, particularly along the electron transfer pathway. Substantial differences are only found at ring V of one bacteriochlorophyll of the 'special pair' and for the secondary quinone, QB. A water chain with a length of about 23 A including 14 water molecules extends from the QB to the cytoplasmic side of the RC. The cofactor arrangement and the mode of binding to the protein seem to be very similar among the non-sulphur bacterial photosynthetic RCs. The functional role of the displaced QB molecule, which might be present as quinol, rather than quinone, is not yet clear. The newly discovered water chain to the QB binding site suggests a pathway for the protonation of the secondary quinone QB.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERA [auth L]281Cereibacter sphaeroidesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
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Go to UniProtKB:  P0C0Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERB [auth M]307Cereibacter sphaeroidesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYNTHETIC REACTION CENTERC [auth H]260Cereibacter sphaeroidesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

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D [auth L],
E [auth L],
F [auth L],
N [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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G [auth L],
O [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10
Query on U10

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H [auth L],
P [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPO
Query on SPO

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Q [auth M]SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
LDA
Query on LDA

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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
PO4
Query on PO4

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M
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE
Query on FE

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L [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
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 = 141.3α = 90
b = 141.3β = 90
c = 187.2γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

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