› 2ji3

X-ray diffraction
1.95Å resolution

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

Released:
DOI: 10.2210/pdb2ji3/pdb
PDB entry 2ji3 coloured by chain, front view.
PDB entry 2ji3 coloured by chain, side view.
PDB entry 2ji3 coloured by chain, top view.
Source organism: Desulfarculus baarsii
Primary publication:
Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme.
Katona G, Carpentier P, Nivière V, Amara P, Adam V, Ohana J, Tsanov N, Bourgeois D
Science 316 449-53 (2007)
PMID: 17446401

Function and Biology Details

Reaction catalysed: 
Reduced rubredoxin + superoxide + 2 H(+) = oxidized rubredoxin + H(2)O(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175122 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Desulfoferrodoxin Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 126 amino acids
Theoretical weight: 14.12 KDa
Source organism: Desulfarculus baarsii
Expression system: Escherichia coli DH5[alpha]
UniProt:
  • Canonical: Q46495 (Residues: 1-126; Coverage: 100%)
Gene names: Deba_2050, dfx, rbo
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand FE 8 x FE
Ligand CA 4 x CA
Ligand NO3 1 x NO3
Ligand PER 3 x PER
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: I222
Unit cell:
a: 69.45Å b: 82.9Å c: 202.66Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.249
Expression system: Escherichia coli DH5[alpha]

Quick links

Citations

7 review citations

Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
Bruijnincx et al. (2008)
6 more

3 mentions without citation

Superoxide dismutases and superoxide reductases.
Sheng et al. (2014)
2 more