› 5hgw

X-ray diffraction
1.6Å resolution

Crystal structure of a peptide deformylase from Burkholderia ambifaria

Released:
DOI: 10.2210/pdb5hgw/pdb
PDB entry 5hgw coloured by chain, front view.
PDB entry 5hgw coloured by chain, side view.
PDB entry 5hgw coloured by chain, top view.
Source organism: Burkholderia ambifaria MC40-6
Entry author: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109464 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 185 amino acids
Theoretical weight: 20.9 KDa
Source organism: Burkholderia ambifaria MC40-6
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B1YSH1 (Residues: 1-177; Coverage: 100%)
Gene names: BamMC406_1925, def
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

3 bound ligands:
Ligand FE 2 x FE
Ligand SO4 8 x SO4
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2221
Unit cell:
a: 116.69Å b: 121.35Å c: 71.29Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.154 0.178
Expression system: Escherichia coli BL21(DE3)

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