1VZH

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: 0.250 
  • R-Value Work: 0.207 

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 photo-reduction.

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

(2004) Structure 12: 1729-1740

  • DOI: 10.1016/j.str.2004.07.013
  • Primary Citation of Related Structures:  

  • 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 c ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DESULFOFERRODOXIN
A, B
126Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14)Mutation(s): 1 
Gene Names: dfx (rbo)
EC: 1.15.1.2
Find proteins for Q46495 (Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14))
Go to UniProtKB:  Q46495
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FC6
Query on FC6

Download SDF File 
Download CCD File 
A, B
HEXACYANOFERRATE(3-)
FERRI(III)HEXACYANIDE
C6 Fe N6
HCMVSLMENOCDCK-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.130α = 90.00
b = 67.650β = 90.00
c = 82.190γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-27
    Type: Initial release
  • Version 1.1: 2011-06-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-28
    Type: Database references, Source and taxonomy