1IO3

CRYSTAL STRUCTURE OF FERRICYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the oxidized cytochrome c(2) from Blastochloris viridis.

Sogabe, S.Miki, K.

(2001) FEBS Lett. 491: 174-179


  • PubMed Abstract: 
  • The crystal structure of the oxidized cytochrome c(2) from Blastochloris (formerly Rhodopseudomonas) viridis was determined at 1.9 A resolution. Structural comparison with the reduced form revealed significant structural changes according to the oxid ...

    The crystal structure of the oxidized cytochrome c(2) from Blastochloris (formerly Rhodopseudomonas) viridis was determined at 1.9 A resolution. Structural comparison with the reduced form revealed significant structural changes according to the oxidation state of the heme iron. Slight perturbation of the polypeptide chain backbone was observed, and the secondary structure and the hydrogen patterns between main-chain atoms were retained. The oxidation state-dependent conformational shifts were localized in the vicinity of the methionine ligand side and the propionate group of the heme. The conserved segment of the polypeptide chain in cytochrome c and cytochrome c(2) exhibited some degree of mobility, interacting with the heme iron atom by the hydrogen bond network. These results indicate that the movement of the internal water molecule conserved in various c-type cytochromes drives the adjustments of side-chain atoms of nearby residue, and the segmental temperature factor changes along the polypeptide chain.


    Related Citations: 
    • Refined crystal structure of ferrocytochrome c2 from Rhodopseudomonas viridis at 1.6 A resolution.
      Miki, K.,Sogabe, S.
      (1995) J.Mol.Biol. 252: 235


    Organizational Affiliation

    Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C2
A
107Blastochloris viridisGene Names: cycA
Find proteins for P00083 (Blastochloris viridis)
Go to UniProtKB:  P00083
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.970α = 90.00
b = 75.970β = 90.00
c = 40.370γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-01-06 
  • Released Date: 2001-04-18 
  • Deposition Author(s): Miki, K., Sogabe, S.

Revision History 

  • Version 1.0: 2001-04-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance