2JI3

X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

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: 10.1126/science.1138885
  • Structures With Same Primary Citation

  • 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 ...

    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
DesulfoferrodoxinA, B, C, D126Desulfarculus baarsiiMutation(s): 1 
Gene Names: dfxrboDeba_2050
EC: 1.15.1.2
Find proteins for Q46495 (Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14))
Explore Q46495 
Go to UniProtKB:  Q46495
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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

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

Download CCD File 
B, C, D
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.45α = 90
b = 82.9β = 90
c = 202.66γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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: 2019-05-15
    Changes: Data collection, Experimental preparation