› 5gro

X-ray diffraction
2Å resolution

Crystal structure of the N-terminal anticodon-binding domain of non-discriminating aspartyl-tRNA synthetase from Helicobacter pylori

Released:
DOI: 10.2210/pdb5gro/pdb
PDB entry 5gro coloured by chain, front view.
PDB entry 5gro coloured by chain, side view.
PDB entry 5gro coloured by chain, top view.
Source organism: Helicobacter pylori 26695
Primary publication:
Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori.
Songsiriritthigul C, Suebka S, Chen CJ, Fuengfuloy P, Chuawong P
Acta Crystallogr F Struct Biol Commun 73 62-69 (2017)
PMID: 28177315

Function and Biology Details

Reaction catalysed: 
ATP + L-aspartate + tRNA(Asx) = AMP + diphosphate + L-aspartyl-tRNA(Asx)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157473 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aspartate--tRNA(Asp/Asn) ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 115 amino acids
Theoretical weight: 12.9 KDa
Source organism: Helicobacter pylori 26695
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P56459 (Residues: 1-104; Coverage: 18%)
Gene names: HP_0617, aspS
Sequence domains: OB-fold nucleic acid binding domain
Structure domains: Nucleic acid-binding proteins

Ligands and Environments

3 bound ligands:
Ligand GOL 2 x GOL
Ligand BUA 1 x BUA
Ligand IMD 1 x IMD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P41212
Unit cell:
a: 61.83Å b: 61.83Å c: 141.376Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.18 0.207
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 mention without citation

Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori.
Songsiriritthigul et al. (2017)