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› 6the

X-ray diffraction
2.87Å resolution

Crystal structure of core domain of four-domain heme-cupredoxin-Cu nitrite reductase from Bradyrhizobium sp. ORS 375

Released:
DOI: 10.2210/pdb6the/pdb
Model geometry
Fit model/data
PDB entry 6the coloured by chain, front view.
PDB entry 6the coloured by chain, side view.
PDB entry 6the coloured by chain, top view.
Source organism: Bradyrhizobium sp. ORS 375
Primary publication:
Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction.
Sasaki D, Watanabe TF, Eady RR, Garratt RC, Antonyuk SV, Hasnain SS
FEBS J 288 262-280 (2021)
PMID: 32255260

Function and Biology Details

Reaction catalysed: 
nitric oxide + Fe(III)-[cytochrome c] + H2O = Fe(II)-[cytochrome c] +nitrite + 2 H(+).
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124699 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Copper-containing nitrite reductase Chain: A
Molecule details ›
Chain: A
Length: 321 amino acids
Theoretical weight: 34.2 KDa
Source organism: Bradyrhizobium sp. ORS 375
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H0SHH5 (Residues: 385-698; Coverage: 45%)
Gene name: BRAO375_2740002
Sequence domains: Multicopper oxidase

Ligands and Environments

7 bound ligands:
Ligand CU 2 x CU
Ligand YB 3 x YB
Ligand ER3 4 x ER3
Ligand TB 1 x TB
Ligand YT3 2 x YT3
Ligand CL 1 x CL
Ligand 9JE 7 x 9JE
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: I23
Unit cell:
a: 125.141Å b: 125.141Å c: 125.141Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.225 0.234
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 citation in other articles

An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Rose et al. (2021)
4 more

5 mentions without citation

AIP1-mediated stress signaling in atherosclerosis and arteriosclerosis.
Zhang et al. (2015)
4 more