› 2zua

X-ray diffraction
2.59Å resolution

Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata

Released:
DOI: 10.2210/pdb2zua/pdb
PDB entry 2zua coloured by chain, front view.
PDB entry 2zua coloured by chain, side view.
PDB entry 2zua coloured by chain, top view.
Source organism: Haloarcula quadrata
Primary publication:
Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases.
Yamamura A, Ichimura T, Kamekura M, Mizuki T, Usami R, Makino T, Ohtsuka J, Miyazono K, Okai M, Nagata K, Tanokura M
Biophys J 96 4692-700 (2009)
PMID: 19486691

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174922 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 174 amino acids
Theoretical weight: 19.74 KDa
Source organism: Haloarcula quadrata
Expression system: Escherichia coli
UniProt:
  • Canonical: Q401C5 (Residues: 1-154; Coverage: 100%)
Gene names: BDK61_3076, 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: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P63
Unit cell:
a: 73.571Å b: 73.571Å c: 214.271Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.222 0.289
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Engineering Robust Cellulases for Tailored Lignocellulosic Degradation Cocktails.
Contreras et al. (2020)
1 more

3 mentions without citation

Salt-bridge energetics in halophilic proteins.
Nayek et al. (2014)
2 more