› 5ah5

X-ray diffraction
2.1Å resolution

Crystal structure of the ternary complex of Agrobacterium radiobacter K84 agnB2 LeuRS-tRNA-LeuAMS

Released:
DOI: 10.2210/pdb5ah5/pdb
PDB entry 5ah5 coloured by chain, front view.
PDB entry 5ah5 coloured by chain, side view.
PDB entry 5ah5 coloured by chain, top view.
Source organisms:
Primary publication:
Structural characterization of antibiotic self-immunity tRNA synthetase in plant tumour biocontrol agent.
Chopra S, Palencia A, Virus C, Schulwitz S, Temple BR, Cusack S, Reader J
Nat Commun 7 12928 (2016)
PMID: 27713402

Function and Biology Details

Reaction catalysed: 
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110834 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Leucine--tRNA ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 822 amino acids
Theoretical weight: 92.35 KDa
Source organism: Agrobacterium radiobacter K84
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B9JQP8 (Residues: 1-814; Coverage: 100%)
Gene names: Arad_15002, agnB2, leuS
Sequence domains:
TRNA-LEU TAA ISOACCEPTOR Chains: C, D
Molecule details ›
Chains: C, D
Length: 84 nucleotides
Theoretical weight: 26.96 KDa
Source organism: Agrobacterium tumefaciens
Expression system: Escherichia coli K-12
Sequence domains: tRNA

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand LSS 2 x LSS
Ligand SO4 5 x SO4
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21
Unit cell:
a: 169.91Å b: 50.32Å c: 170.52Å
α: 90° β: 93.48° γ: 90°
R-values:
R R work R free
0.196 0.194 0.237
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli K-12

Quick links

Citations

7 review citations

Aminoacyl-tRNA Synthetases as Valuable Targets for Antimicrobial Drug Discovery.
Pang et al. (2021)
6 more

4 mentions without citation

Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs.
Tragni et al. (2022)
3 more