› 1dy7

X-ray diffraction
1.6Å resolution

Cytochrome cd1 Nitrite Reductase, CO complex

Released:
DOI: 10.2210/pdb1dy7/pdb
PDB entry 1dy7 coloured by chain, front view.
PDB entry 1dy7 coloured by chain, side view.
PDB entry 1dy7 coloured by chain, top view.
Source organism: Paracoccus pantotrophus
Primary publication:
Proton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and X-ray crystallography study.
Sjögren T, Svensson-Ek M, Hajdu J, Brzezinski P
Biochemistry 39 10967-74 (2000)
PMID: 10998233

Function and Biology Details

Reactions catalysed: 
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
NH(3) + H(2)O + acceptor = hydroxylamine + reduced acceptor
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159836 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nitrite reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 567 amino acids
Theoretical weight: 62.55 KDa
Source organism: Paracoccus pantotrophus
UniProt:
  • Canonical: P72181 (Residues: 30-596; Coverage: 100%)
Gene name: nirS
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand HEC 1 x HEC

Cofactor: Ligand DHE 2 x DHE
3 bound ligands:
Ligand CMO 2 x CMO
Ligand GOL 3 x GOL
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 106.94Å b: 61.04Å c: 100.39Å
α: 90° β: 111.77° γ: 90°
R-values:
R R work R free
0.178 0.178 0.199

Quick links

Citations

1 review citation

Cryocrystallography of metalloprotein reaction intermediates.
Wilmot et al. (2002)
3 other articles