› 5f7a

X-ray diffraction
1.54Å resolution

Nitrite complex structure of copper nitrite reductase from Alcaligenes faecalis determined at 293 K

Released:
DOI: 10.2210/pdb5f7a/pdb
PDB entry 5f7a coloured by chain, front view.
PDB entry 5f7a coloured by chain, side view.
PDB entry 5f7a coloured by chain, top view.
Source organism: Alcaligenes faecalis
Primary publication:
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.
Fukuda Y, Tse KM, Nakane T, Nakatsu T, Suzuki M, Sugahara M, Inoue S, Masuda T, Yumoto F, Matsugaki N, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Murphy ME, Inoue T, Iwata S, Mizohata E
Proc Natl Acad Sci U S A 113 2928-33 (2016)
PMID: 26929369

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-153659 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 342 amino acids
Theoretical weight: 37.02 KDa
Source organism: Alcaligenes faecalis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38501 (Residues: 40-376; Coverage: 98%)
Gene names: nir, nirK
Sequence domains:
Structure domains: Cupredoxins - blue copper proteins

Ligands and Environments

2 bound ligands:
Ligand CU 6 x CU
Ligand NO2 3 x NO2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P212121
Unit cell:
a: 62.86Å b: 103.686Å c: 146.972Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.152 0.151 0.18
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules.
Chapman HN. (2019)
9 more

1 mention without citation

Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography.
Fukuda et al. (2016)