2JI2

X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.

Katona, G.Carpentier, P.Niviere, V.Amara, P.Adam, V.Ohana, J.Tsanov, N.Bourgeois, D.

(2007) Science 316: 449-453

  • DOI: 10.1126/science.1138885
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radi ...

    Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.


    Organizational Affiliation

    Institut de Biologie Structurale (IBS) Jean-Pierre Ebel, Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Desulfoferrodoxin
A, B, C, D
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download SDF File 
Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B, C, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B, C, D
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 70.470α = 90.00
b = 82.870β = 90.00
c = 201.950γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
CNSrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    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, Structure summary
  • Version 1.4: 2018-06-27
    Type: Data collection, Derived calculations
  • Version 1.5: 2019-05-08
    Type: Data collection, Experimental preparation