1VZG

Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray induced photoreduction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Superoxide Reductase Bound to Ferrocyanide and Active Site Expansion Upon X-Ray Induced Photoreduction

Adam, V.Royant, A.Niviere, V.Molina-Heredia, F.P.Bourgeois, D.

(2004) Structure 12: 1729

  • DOI: https://doi.org/10.1016/j.str.2004.07.013
  • Primary Citation of Related Structures:  
    1VZG, 1VZH, 1VZI

  • PubMed Abstract: 

    Some sulfate-reducing and microaerophilic bacteria rely on the enzyme superoxide reductase (SOR) to eliminate the toxic superoxide anion radical (O2*-). SOR catalyses the one-electron reduction of O2*- to hydrogen peroxide at a nonheme ferrous iron center. The structures of Desulfoarculus baarsii SOR (mutant E47A) alone and in complex with ferrocyanide were solved to 1.15 and 1.7 A resolution, respectively. The latter structure, the first ever reported of a complex between ferrocyanide and a protein, reveals that this organo-metallic compound entirely plugs the SOR active site, coordinating the active iron through a bent cyano bridge. The subtle structural differences between the mixed-valence and the fully reduced SOR-ferrocyanide adducts were investigated by taking advantage of the photoelectrons induced by X-rays. The results reveal that photo-reduction from Fe(III) to Fe(II) of the iron center, a very rapid process under a powerful synchrotron beam, induces an expansion of the SOR active site.


  • Organizational Affiliation

    LCCP, UMR 5075, IBS-CEA/CNRS/Université J. Fourier, 41 Avenue Jules Horowitz, 38027 Grenoble, Cedex 1, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DESULFOFERRODOXIN
A, B
126Desulfarculus baarsiiMutation(s): 1 
EC: 1.15.1.2
UniProt
Find proteins for Q46495 (Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / LMG 7858 / VKM B-1802 / 2st14))
Explore Q46495 
Go to UniProtKB:  Q46495
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46495
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.13α = 90
b = 67.65β = 90
c = 82.19γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-27
    Type: Initial release
  • Version 1.1: 2011-06-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description