› 4yst

X-ray diffraction
1.34Å resolution

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 24.9 MGy

Released:
DOI: 10.2210/pdb4yst/pdb
PDB entry 4yst coloured by chain, front view.
PDB entry 4yst coloured by chain, side view.
PDB entry 4yst coloured by chain, top view.
Source organism: Geobacillus thermodenitrificans NG80-2
Primary publication:
Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography.
Fukuda Y, Tse KM, Suzuki M, Diederichs K, Hirata K, Nakane T, Sugahara M, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Matsumura H, Inoue T, Iwata S, Mizohata E
J Biochem 159 527-38 (2016)
PMID: 26769972

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:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107338 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 323 amino acids
Theoretical weight: 35.52 KDa
Source organism: Geobacillus thermodenitrificans NG80-2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A4IL26 (Residues: 31-352; Coverage: 97%)
Gene names: GTNG_0650, nirK
Sequence domains:
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

3 bound ligands:
Ligand CU 6 x CU
Ligand MPD 1 x MPD
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: R3
Unit cell:
a: 115.177Å b: 115.177Å c: 84.376Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.156 0.155 0.185
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Recent structural insights into the function of copper nitrite reductases.
Horrell et al. (2017)
2 more

1 mention without citation

Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography.
Fukuda et al. (2016)