› 3ztr

X-ray diffraction
2.3Å resolution

Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FIRST STAGE OF RADIATION DAMAGE)

Released:
DOI: 10.2210/pdb3ztr/pdb
PDB entry 3ztr coloured by chain, front view.
PDB entry 3ztr coloured by chain, side view.
PDB entry 3ztr coloured by chain, top view.
Source organism: Aquifex aeolicus
Primary publication:
An intersubunit disulfide bridge stabilizes the tetrameric nucleoside diphosphate kinase of Aquifex aeolicus.
Boissier F, Georgescauld F, Moynié L, Dupuy JW, Sarger C, Podar M, Lascu I, Giraud MF, Dautant A
Proteins 80 1658-68 (2012)
PMID: 22467275

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130509 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 142 amino acids
Theoretical weight: 15.96 KDa
Source organism: Aquifex aeolicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O67528 (Residues: 1-142; Coverage: 100%)
Gene names: aq_1590, 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: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P6122
Unit cell:
a: 200.71Å b: 200.71Å c: 246.731Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.193 0.192 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

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