› 2qmi

X-ray diffraction
2.2Å resolution

Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi

Released:
DOI: 10.2210/pdb2qmi/pdb
PDB entry 2qmi coloured by chain, front view.
PDB entry 2qmi coloured by chain, side view.
PDB entry 2qmi coloured by chain, top view.
Source organism: Pyrococcus abyssi
Primary publication:
Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.
Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C
PLoS One 4 e4712 (2009)
PMID: 19266066

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194171 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pbp related beta-lactamase (Penicillin-binding protein) Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 447 amino acids
Theoretical weight: 50.5 KDa
Source organism: Pyrococcus abyssi
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9V2D6 (Residues: 1-447; Coverage: 100%)
Gene names: PAB0087, pbp
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand LU 17 x LU
Ligand DO3 4 x DO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P1
Unit cell:
a: 100.94Å b: 105.63Å c: 112.92Å
α: 72.17° β: 66.51° γ: 81.39°
R-values:
R R work R free
0.196 0.196 0.241
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales.
Leigh et al. (2011)
2 more

13 mentions without citation

ClbP is a prototype of a peptidase subgroup involved in biosynthesis of nonribosomal peptides.
Dubois et al. (2011)
12 more