1RQK | pdb_00001rqk

Structure of the reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1 reconstituted with 3,4-dihydrospheroidene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.194 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

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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 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.

Macromolecule Content 

  • Total Structure Weight: 104.66 kDa 
  • Atom Count: 7,522 
  • Modeled Residue Count: 824 
  • Deposited Residue Count: 848 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
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
Find similar proteins by:|  3D Structure
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
P [auth M]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL

Query on BCL



Download:Ideal Coordinates CCD File
D [auth L],
E [auth L],
K [auth M],
L [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
F [auth L],
M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10

Query on U10



Download:Ideal Coordinates CCD File
G [auth L],
N [auth M]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
SP2

Query on SP2



Download:Ideal Coordinates CCD File
O [auth M]3,4-DIHYDROSPHEROIDENE
C41 H62 O
IUUXWKRRZDDNQG-DJSFQYKBSA-N
LDA

Query on LDA



Download:Ideal Coordinates CCD File
H [auth L]
I [auth L]
Q [auth M]
R [auth M]
S [auth M]
H [auth L],
I [auth L],
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
FE

Query on FE



Download:Ideal Coordinates CCD File
J [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.194 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.718α = 90
b = 141.718β = 90
c = 187.179γ = 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