› 4gxh

X-ray diffraction
2.7Å resolution

Crystal Structure of a Pyrrolidone-carboxylate peptidase 1 (target ID NYSGRC-012831) from Xenorhabdus bovienii SS-2004

Released:
DOI: 10.2210/pdb4gxh/pdb
PDB entry 4gxh coloured by chain, front view.
PDB entry 4gxh coloured by chain, side view.
PDB entry 4gxh coloured by chain, top view.
Source organism: Xenorhabdus bovienii SS-2004
Entry authors: Ghosh A, Almo SC, New York Structural Genomics Research Consortium (NYSGRC)

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112559 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrrolidone-carboxylate peptidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 216 amino acids
Theoretical weight: 23.37 KDa
Source organism: Xenorhabdus bovienii SS-2004
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D3V0W1 (Residues: 1-215; Coverage: 100%)
Gene names: XBJ1_1667, pcp
Sequence domains: Pyroglutamyl peptidase
Structure domains: Peptidase C15, pyroglutamyl peptidase I-like

Ligands and Environments

2 bound ligands:
Ligand PO4 5 x PO4
Ligand CL 4 x CL
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P4322
Unit cell:
a: 117.179Å b: 117.179Å c: 186.615Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.219
Expression system: Escherichia coli BL21(DE3)

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