› 5cy7

X-ray diffraction
2.4Å resolution

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryze pv oryze, in complex with fragment 275

Released:
DOI: 10.2210/pdb5cy7/pdb
PDB entry 5cy7 coloured by chain, front view.
PDB entry 5cy7 coloured by chain, side view.
PDB entry 5cy7 coloured by chain, top view.
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Entry authors: Ngo HPT, Kang LW

Function and Biology Details

Reaction catalysed: 
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
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-177161 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chain: A
Molecule details ›
Chain: A
Length: 171 amino acids
Theoretical weight: 19.1 KDa
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5H3Z2 (Residues: 42-212; Coverage: 81%)
Gene names: XOO1075, def
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

4 bound ligands:
Ligand CD 3 x CD
Ligand ACT 1 x ACT
Ligand 56U 1 x 56U
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P6122
Unit cell:
a: 58.823Å b: 58.823Å c: 264.034Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.181 0.212
Expression system: Escherichia coli

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