› 8ryv

X-ray diffraction
1.45Å resolution

MSOX movie series dataset 10 (11.5 MGy) for nitrite bound BrJNiR (Cu containing nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 at pH 8.

Released:
DOI: 10.2210/pdb8ryv/pdb
PDB entry 8ryv coloured by chain, front view.
PDB entry 8ryv coloured by chain, side view.
PDB entry 8ryv coloured by chain, top view.
Source organism: Bradyrhizobium sp.
Primary publication:
Spectroscopically validated pH-dependent MSOX movies provide detailed mechanism of copper nitrite reductases.
Rose SL, Martín Ferroni F, Horrell S, Dante Brondino C, Eady RR, Jaho S, Hough MA, Owen RL, Antonyuk SV, Samar Hasnain S
J Mol Biol 168706 (2024)
PMID: 39002715

Function and Biology Details

Reaction catalysed: 
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-247472 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 367 amino acids
Theoretical weight: 39.76 KDa
Source organism: Bradyrhizobium sp.
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q89EJ6 (Residues: 1-367; Coverage: 100%)
Gene name: nirK
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
4 bound ligands:
Ligand CU 2 x CU
Ligand NO 1 x NO
Ligand NO2 1 x NO2
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P63
Unit cell:
a: 104.3Å b: 104.3Å c: 64.47Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.142 0.14 0.164
Expression system: Escherichia coli BL21

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