› 2vm3

X-ray diffraction
1.8Å resolution

Structure of Alcaligenes xylosoxidans in space group R3 - 1 of 2

Released:
DOI: 10.2210/pdb2vm3/pdb
PDB entry 2vm3 coloured by chain, front view.
PDB entry 2vm3 coloured by chain, side view.
PDB entry 2vm3 coloured by chain, top view.
Source organism: Achromobacter xylosoxidans
Primary publication:
Crystallography with online optical and X-ray absorption spectroscopies demonstrates an ordered mechanism in copper nitrite reductase.
Hough MA, Antonyuk SV, Strange RW, Eady RR, Hasnain SS
J Mol Biol 378 353-61 (2008)
PMID: 18353369

Function and Biology Details

Reaction catalysed: 
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130622 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 336 amino acids
Theoretical weight: 36.57 KDa
Source organism: Achromobacter xylosoxidans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O68601 (Residues: 25-360; Coverage: 100%)
Gene names: O9570_16215, nir, nirK
Sequence domains:
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

3 bound ligands:
Ligand CU 2 x CU
Ligand ZN 1 x ZN
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX10.1
Spacegroup: R3
Unit cell:
a: 89.941Å b: 89.941Å c: 143.732Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.186 0.184 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Gating mechanisms for biological electron transfer: integrating structure with biophysics reveals the nature of redox control in cytochrome P450 reductase and copper-dependent nitrite reductase.
Leferink et al. (2012)
5 more