› 1v3y

X-ray diffraction
1.81Å resolution

The crystal structure of peptide deformylase from Thermus thermophilus HB8

Released:
DOI: 10.2210/pdb1v3y/pdb
PDB entry 1v3y coloured by chain, front view.
PDB entry 1v3y coloured by chain, side view.
PDB entry 1v3y coloured by chain, top view.
Source organism: Thermus thermophilus
Entry authors: Kamo M, Kudo N, Lee WC, Ito K, Motoshim H, Tanokura M, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155083 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 192 amino acids
Theoretical weight: 22.17 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P43522 (Residues: 1-192; Coverage: 100%)
Gene name: def
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

No bound ligands
1 modified residue:
Ligand OCS 2 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P43
Unit cell:
a: 62.582Å b: 62.582Å c: 105.271Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.208
Expression system: Escherichia coli

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