› 7zcn

X-ray diffraction
1.19Å resolution

Nitrite-bound MSOX movie series dataset 1 (0.8 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - nitrite (start)

Released:
DOI: 10.2210/pdb7zcn/pdb
PDB entry 7zcn coloured by chain, front view.
PDB entry 7zcn coloured by chain, side view.
PDB entry 7zcn coloured by chain, top view.
Source organism: Bradyrhizobium sp. ORS 375
Primary publication:
Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Rose SL, Baba S, Okumura H, Antonyuk SV, Sasaki D, Hedison TM, Shanmugam M, Heyes DJ, Scrutton NS, Kumasaka T, Tosha T, Eady RR, Yamamoto M, Hasnain SS
OpenAccess logo Proc Natl Acad Sci U S A 119 e2205664119 (2022)
PMID: 35862453

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-124700 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 350 amino acids
Theoretical weight: 38.29 KDa
Source organism: Bradyrhizobium sp. ORS 375
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H0SLX7 (Residues: 25-364; Coverage: 100%)
Gene names: BRAO375_4030011, nirK
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
4 bound ligands:
Ligand SO4 11 x SO4
Ligand CU 2 x CU
Ligand NO2 4 x NO2
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P213
Unit cell:
a: 106.725Å b: 106.725Å c: 106.725Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.109 0.108 0.134
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 mention without citation

Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Rose et al. (2022)