› 2dbo

X-ray diffraction
2.76Å resolution

Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Aquifex aeolicus

Released:
DOI: 10.2210/pdb2dbo/pdb
PDB entry 2dbo coloured by chain, front view.
PDB entry 2dbo coloured by chain, side view.
PDB entry 2dbo coloured by chain, top view.
Source organism: Aquifex aeolicus VF5
Entry authors: Ishii T, Shibata R, Bessho Y, Shirouzu M, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
A D-aminoacyl-tRNA + H(2)O = a D-amino acid + tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130376 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-aminoacyl-tRNA deacylase Chain: A
Molecule details ›
Chain: A
Length: 148 amino acids
Theoretical weight: 16.99 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli
UniProt:
  • Canonical: O66742 (Residues: 1-148; Coverage: 100%)
Gene names: aq_428, dtd
Sequence domains: D-Tyr-tRNA(Tyr) deacylase
Structure domains: D-tyrosyl-tRNA(Tyr) deacylase

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P6522
Unit cell:
a: 76.01Å b: 76.01Å c: 133.754Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.23 0.23 0.284
Expression system: Escherichia coli

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