1PRC

CRYSTALLOGRAPHIC REFINEMENT AT 2.3 ANGSTROMS RESOLUTION AND REFINED MODEL OF THE PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic refinement at 2.3 A resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis.

Deisenhofer, J.Epp, O.Sinning, I.Michel, H.

(1995) J.Mol.Biol. 246: 429-457

  • DOI: 10.1006/jmbi.1994.0097
  • Also Cited By: 1DXR, 2JBL

  • PubMed Abstract: 
  • The atomic model of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis has been refined to an R-value of 0.193 at 2.3 A resolution. The refined model contains 10,288 non-hydrogen atoms; 10,045 of these have well def ...

    The atomic model of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis has been refined to an R-value of 0.193 at 2.3 A resolution. The refined model contains 10,288 non-hydrogen atoms; 10,045 of these have well defined electron density. A Luzzati-plot indicates an average co-ordinate error of 0.26 A. During refinement, the positions of a partially ordered carotenoid, a unibiquinone in the partially occupied QB site, a detergent molecule, seven putative sulphate ions, and 201 water molecules were found. More than half of these waters are bound at interfaces between protein subunits and therefore contribute significantly to subunit interactions. Water molecules also play important structural and probably functional roles in the environment of some of the cofactors. Two water molecules form hydrogen bonds to the accessory bacteriochlorophylls and to the protein in the vicinity of the special pair of bacteriophylls, the primary electron donor. A group of about 10 water molecules is bound near the binding site of the secondary quinone QB. These waters are likely to participate in the transfer of protons to the doubly reduced QB.


    Related Citations: 
    • X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 Angstroms Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis
      Deisenhofer, J.,Epp, O.,Miki, K.,Huber, R.,Michel, H.
      (1984) J.Mol.Biol. 180: 385
    • The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis
      Deisenhofer, J.,Michel, H.
      (1989) Science 245: 1463
    • Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution
      Deisenhofer, J.,Epp, O.,Miki, K.,Huber, R.,Michel, H.
      (1985) Nature 318: 618
    • Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
      Michel, H.
      (1982) J.Mol.Biol. 158: 567


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, F.R.G.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
C
336Blastochloris viridisGene Names: pufC (cytC)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P07173 (Blastochloris viridis)
Go to UniProtKB:  P07173
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
L
273Blastochloris viridisGene Names: pufL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P06009 (Blastochloris viridis)
Go to UniProtKB:  P06009
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
M
323Blastochloris viridisGene Names: pufM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P06010 (Blastochloris viridis)
Go to UniProtKB:  P06010
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PHOTOSYNTHETIC REACTION CENTER
H
258Blastochloris viridisGene Names: puhA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosynthetic Reaction Centers
Protein: 
Photosynthetic Reaction Center
Find proteins for P06008 (Blastochloris viridis)
Go to UniProtKB:  P06008
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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H, M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UQ1
Query on UQ1

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Download CCD File 
L
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
 Ligand Interaction
NS1
Query on NS1

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M
15-trans-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-HFHFAFRXSA-N
 Ligand Interaction
LDA
Query on LDA

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H, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FE
Query on FE

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M
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MQ7
Query on MQ7

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M
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
BPB
Query on BPB

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L, M
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
 Ligand Interaction
BCB
Query on BCB

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L, M
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-LQPBATPMDK
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
H
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 223.500α = 90.00
b = 223.500β = 90.00
c = 113.600γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1989-01-09
    Type: Initial release
  • Version 1.1: 2008-03-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2014-08-13
    Type: Other