1RG5

Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Protein Regulation of Carotenoid Binding: Gatekeeper and Locking Amino Acid Residues in Reaction Centers of Rhodobacter sphaeroides

Roszak, A.W.McKendrick, K.Gardiner, A.T.Mitchell, I.A.Isaacs, N.W.Cogdell, R.J.Hashimoto, H.Frank, H.A.

(2004) Structure 12: 765-773

  • DOI: https://doi.org/10.1016/j.str.2004.02.037
  • Primary Citation of Related Structures:  
    1RG5, 1RGN, 1RQK

  • PubMed Abstract: 

    X-ray diffraction was used to determine high-resolution structures of the reaction center (RC) complex from the carotenoidless mutant, Rb. sphaeroides R-26.1, without or reconstituted with carotenoids. The results are compared with the structure of the RC from a semiaerobically grown Rb. sphaeroides strain 2.4.1. The investigation reveals the structure of the carotenoid in the different protein preparations, the nature of its binding site, and a plausible mechanism by which the carotenoid is incorporated unidirectionally in its characteristic geometric configuration. The structural data suggest that the accessibility of the carotenoid to the binding site is controlled by a specific "gatekeeper" residue which allows the carotenoid to approach the binding site from only one direction. Carotenoid binding to the protein is secured by hydrogen bonding to a separate "locking" amino acid. The study reveals the specific molecular interactions that control how the carotenoid protects the photosynthetic apparatus against photo-induced oxidative destruction.


  • Organizational Affiliation

    Department of Chemistry, IBLS, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainA [auth L]281Cereibacter sphaeroidesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
Explore P0C0Y8 
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
Reaction center protein M chainB [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
Reaction center protein H chainC [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
CDL
Query on CDL

Download Ideal Coordinates CCD File 
O [auth M]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
Query on BCL

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

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

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G [auth L],
M
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
LDA
Query on LDA

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P [auth M]
Q [auth M]
R [auth M]
S [auth M]
T [auth M]
P [auth M],
Q [auth M],
R [auth M],
S [auth M],
T [auth M],
U [auth H]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO
Query on HTO

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H [auth L],
N [auth M]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
FE
Query on FE

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I [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.033α = 90
b = 144.033β = 90
c = 190.072γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations