1YST

STRUCTURE OF THE PHOTOCHEMICAL REACTION CENTER OF A SPHEROIDENE CONTAINING PURPLE BACTERIUM, RHODOBACTER SPHAEROIDES Y, AT 3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the photochemical reaction centre of a spheroidene-containing purple-bacterium, Rhodobacter sphaeroides Y, at 3 A resolution.

Arnoux, B.Gaucher, J.F.Ducruix, A.Reiss-Husson, F.

(1995) Acta Crystallogr.,Sect.D 51: 368-379

  • DOI: 10.1107/S0907444994013120

  • PubMed Abstract: 
  • The crystal structure of the photochemical reaction centre from Rhodobacter sphaeroides Y, a carotenoid-containing wild-type purple bacterium, has been determined at 3 A resolution. This membrane complex consists of three subunits (281, 307 and 260 r ...

    The crystal structure of the photochemical reaction centre from Rhodobacter sphaeroides Y, a carotenoid-containing wild-type purple bacterium, has been determined at 3 A resolution. This membrane complex consists of three subunits (281, 307 and 260 residues, respectively) and ten cofactors. It was crystallized in presence of beta-D-octylglucoside. The crystals are orthorhombic with unit-cell dimensions, a = 143.7, b = 139.8, c = 78.7 A, space group P2(1)2(1)2(1) with four molecules in the unit cell. Refinement of the structure by X-PLOR and manual reconstructions yielded an R value of 22.1% for 19630 reflections between 7 and 3 A. The secondary structure is highly homologous to those determined for Rhodopseudomonas viridis (Protein Data Bank entry 1PRC) and Rhodobacter sphaeroides R26 (Protein Data Bank entry 4RCR) reaction centres. In the latter two structures one Fe(2+) ion located between the two quinones is coordinated by four histidines and one glutamic acid. In the Rhodobacter sphaeroides Y structure, Mn(2+) occupies the same position with identical ligands and geometry. The carotenoid conformation which is a non-planar 15-15'-cis spheroidene molecule in our structure differs from the 13-14-cis 2,4-dihydroneusporene in the Rhodopseudomonas viridis structure.


    Related Citations: 
    • Primary Characterization by X-Ray Diffraction of Crystals of Photochemical Reaction Centers from Wild-Type Rhodopseudomonas Spheroides
      Ducruix, A.,Reiss-Husson, F.
      (1987) J.Mol.Biol. 193: 419


    Organizational Affiliation

    Laboratoire de Biologie Structurale, CNRS, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER (L SUBUNIT)
L
273Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER (M SUBUNIT)
M
305Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER (H SUBUNIT)
H
260Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
M
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 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
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: 3 Å
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 143.700α = 90.00
b = 139.800β = 90.00
c = 78.650γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance