› 3f7k

X-ray diffraction
1.35Å resolution

X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

Released:
DOI: 10.2210/pdb3f7k/pdb
PDB entry 3f7k coloured by chain, front view.
PDB entry 3f7k coloured by chain, side view.
PDB entry 3f7k coloured by chain, top view.
Source organism: Alvinella pompejana
Primary publication:
Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.
Shin DS, Didonato M, Barondeau DP, Hura GL, Hitomi C, Berglund JA, Getzoff ED, Cary SC, Tainer JA
J Mol Biol 385 1534-55 (2009)
PMID: 19063897

Function and Biology Details

Reaction catalysed: 
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110314 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Superoxide dismutase [Cu-Zn] Chain: A
Molecule details ›
Chain: A
Length: 152 amino acids
Theoretical weight: 15.72 KDa
Source organism: Alvinella pompejana
Expression system: Escherichia coli
UniProt:
  • Canonical: B6CHW7 (Residues: 2-153; Coverage: 99%)
Gene name: SOD1
Sequence domains: Copper/zinc superoxide dismutase (SODC)
Structure domains: Superoxide dismutase, copper/zinc binding domain

Ligands and Environments

6 bound ligands:
Ligand CU1 1 x CU1
Ligand CU 1 x CU
Ligand ZN 1 x ZN
Ligand NA 1 x NA
Ligand SO4 4 x SO4
Ligand PEO 1 x PEO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P6122
Unit cell:
a: 62.563Å b: 62.563Å c: 163.745Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.147 not available 0.176
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Small-angle scattering for structural biology--expanding the frontier while avoiding the pitfalls.
Jacques et al. (2010)
7 more

3 mentions without citation

Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.
Shin et al. (2009)
2 more