› 1nb2

X-ray diffraction
2.2Å resolution

Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans

Released:
DOI: 10.2210/pdb1nb2/pdb
PDB entry 1nb2 coloured by chain, front view.
PDB entry 1nb2 coloured by chain, side view.
PDB entry 1nb2 coloured by chain, top view.
Source organism: Virgibacillus halodenitrificans
Primary publication:
Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase.
Chen CJ, Liu MY, Chang T, Chang WC, Wang BC, Le Gall J
J Struct Biol 142 247-55 (2003)
PMID: 12713952

Function and Biology Details

Reaction catalysed: 
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181939 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chain: A
Molecule details ›
Chain: A
Length: 150 amino acids
Theoretical weight: 14.88 KDa
Source organism: Virgibacillus halodenitrificans
UniProt:
  • Canonical: Q7SIA9 (Residues: 1-150; Coverage: 100%)
Gene name: ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL17B2
Spacegroup: P4332
Unit cell:
a: 114.07Å b: 114.07Å c: 114.07Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.213 0.254

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Citations

1 review citation

Structure, Folding and Stability of Nucleoside Diphosphate Kinases.
Georgescauld et al. (2020)
6 other articles