› 4l38

X-ray diffraction
1.8Å resolution

Nitrite complex of TvNiR, low dose data set

Released:
DOI: 10.2210/pdb4l38/pdb
PDB entry 4l38 coloured by chain, front view.
PDB entry 4l38 coloured by chain, side view.
PDB entry 4l38 coloured by chain, top view.
Source organism: Thioalkalivibrio nitratireducens DSM 14787
Entry authors: Trofimov AA, Polyakov KM, Lazarenko VA, Popov AN, Tikhonova TV, Tikhonov AV, Popov VO

Function and Biology Details

Reaction catalysed: 
NH(3) + 2 H(2)O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125732 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytochrome c-552 Chains: A, B
Molecule details ›
Chains: A, B
Length: 520 amino acids
Theoretical weight: 58.93 KDa
Source organism: Thioalkalivibrio nitratireducens DSM 14787
UniProt:
  • Canonical: L0DSL2 (Residues: 33-551; Coverage: 99%)
Gene names: TVNIR_0259, nir
Sequence domains: Cytochrome c552
Structure domains:

Ligands and Environments


Cofactor: Ligand HEC 16 x HEC
5 bound ligands:
Ligand NO2 6 x NO2
Ligand CA 4 x CA
Ligand MPD 2 x MPD
Ligand GOL 5 x GOL
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P213
Unit cell:
a: 193.97Å b: 193.97Å c: 193.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.153 0.17

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