› 3kk0

X-ray diffraction
2.65Å resolution

Crystal structure of partially folded intermediate state of peptidyl-tRNA hydrolase from Mycobacterium smegmatis

Released:
DOI: 10.2210/pdb3kk0/pdb
PDB entry 3kk0 coloured by chain, front view.
PDB entry 3kk0 coloured by chain, side view.
PDB entry 3kk0 coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Entry authors: Kumar A, Singh N, Yadav R, Sharma S, Arora A, Singh TP

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106442 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidyl-tRNA hydrolase Chain: A
Molecule details ›
Chain: A
Length: 191 amino acids
Theoretical weight: 20.27 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0R3D3 (Residues: 1-191; Coverage: 100%)
Gene names: MSMEG_5432, MSMEI_5283, pth
Sequence domains: Peptidyl-tRNA hydrolase
Structure domains: Peptidyl-tRNA hydrolase

Ligands and Environments

4 bound ligands:
Ligand IPA 3 x IPA
Ligand EDO 4 x EDO
Ligand PEG 1 x PEG
Ligand BME 1 x BME
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P212121
Unit cell:
a: 50.006Å b: 65.597Å c: 68.69Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.223 0.241
Expression system: Escherichia coli BL21(DE3)

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