› 3ayf

X-ray diffraction
2.5Å resolution

Crystal structure of nitric oxide reductase

Released:
DOI: 10.2210/pdb3ayf/pdb
PDB entry 3ayf coloured by chain, front view.
PDB entry 3ayf coloured by chain, side view.
PDB entry 3ayf coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.
Matsumoto Y, Tosha T, Pisliakov AV, Hino T, Sugimoto H, Nagano S, Sugita Y, Shiro Y
Nat Struct Mol Biol 19 238-45 (2012)
PMID: 22266822

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-109980 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytochrome oxidase subunit I profile domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 800 amino acids
Theoretical weight: 91.37 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: B3Y963 (Residues: 1-792; Coverage: 100%)
Gene name: norZ
Sequence domains: Cytochrome C and Quinol oxidase polypeptide I
Structure domains: Cytochrome c oxidase-like, subunit I domain

Ligands and Environments

6 bound ligands:
Ligand HEM 2 x HEM
Ligand ZN 1 x ZN
Ligand CA 1 x CA
Ligand BOG 3 x BOG
Ligand EPE 1 x EPE
Ligand LOP 2 x LOP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2221
Unit cell:
a: 110.409Å b: 149.648Å c: 151.108Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.244 0.244 0.282
Expression system: Escherichia coli

Quick links

Citations

8 review citations

The microbial nitrogen-cycling network.
Kuypers et al. (2018)
7 more

12 mentions without citation

Oxygen Activation and Energy Conservation by Cytochrome c Oxidase.
Wikström et al. (2018)
11 more