› 5b1j

X-ray diffraction
3Å resolution

Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin

Released:
DOI: 10.2210/pdb5b1j/pdb
PDB entry 5b1j coloured by chain, front view.
PDB entry 5b1j coloured by chain, side view.
PDB entry 5b1j coloured by chain, top view.
Source organisms:
Primary publication:
Structure and Function of Copper Nitrite Reductase
Nojiri M
Metalloenzymes in denitrification: Applications and Environmental impacts 91-113 (2016)

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 analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108465 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Copper-containing nitrite reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 336 amino acids
Theoretical weight: 36.57 KDa
Source organism: Achromobacter xylosoxidans
UniProt:
  • Canonical: O68601 (Residues: 25-360; Coverage: 100%)
Gene names: O9570_16215, nir, nirK
Sequence domains:
Structure domains: Cupredoxins - blue copper proteins
Blue (type 1) copper domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 124 amino acids
Theoretical weight: 13.59 KDa
Source organism: Hyphomicrobium denitrificans
UniProt:
  • Canonical: A7VL37 (Residues: 27-150; Coverage: 100%)
Gene name: paz
Sequence domains: Copper binding proteins, plastocyanin/azurin family
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

1 bound ligand:
Ligand CU 5 x CU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P213
Unit cell:
a: 153.226Å b: 153.226Å c: 153.226Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.171 0.233

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