1RGN

Structure of the reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1 reconstituted with spheroidene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.str.2004.02.037
  • Primary Citation of Related Structures:  1RG5, 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 t ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein L chain
L
281Rhodobacter sphaeroidesGene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein M chain
M
307Rhodobacter sphaeroidesGene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein H chain
H
260Rhodobacter sphaeroidesGene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
M
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
U10
Query on U10

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Download CCD File 
L, M
UBIQUINONE-10
Coenzyme Q10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
BCL
Query on BCL

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Download CCD File 
L, M
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
LDA
Query on LDA

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Download CCD File 
H, L, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
M
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
BPH
Query on BPH

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Download CCD File 
L, M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
SPO
Query on SPO

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Download CCD File 
M
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 139.817α = 90.00
b = 139.817β = 90.00
c = 184.047γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation