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: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.6 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: https://doi.org/10.1126/science.1138885
  • Primary Citation of Related Structures:  
    2JI1, 2JI2, 2JI3

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Desulfoferrodoxin
A, B, C, D
126Desulfarculus baarsiiMutation(s): 1 
Gene Names: dfxrboDeba_2050
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
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
S [auth D]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
Q [auth C],
T [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
R [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth B],
N [auth C],
O [auth C],
P [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.47α = 90
b = 82.87β = 90
c = 201.95γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2018-06-27
    Changes: Data collection, Derived calculations
  • Version 1.5: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description