› 8rfu

X-ray diffraction
2.18Å resolution

Low pH (5.5) nitrite-bound MSOX movie series dataset 40 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [24.4 MGy] - water ligand + decarboxylated AspCAT (final)

Released:
DOI: 10.2210/pdb8rfu/pdb
PDB entry 8rfu coloured by chain, front view.
PDB entry 8rfu coloured by chain, side view.
PDB entry 8rfu coloured by chain, top view.
Source organism: Bradyrhizobium diazoefficiens USDA 110
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:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-567619 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 340 amino acids
Theoretical weight: 37.11 KDa
Source organism: Bradyrhizobium diazoefficiens USDA 110
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q89EJ6 (Residues: 29-367; Coverage: 100%)
Gene name: nirK
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
3 bound ligands:
Ligand CU 2 x CU
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: 104.52Å b: 104.52Å c: 64.69Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.186 0.222
Expression system: Escherichia coli BL21(DE3)

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