› 3mfd

X-ray diffraction
1.75Å resolution

The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine carboxypeptidase from Bacillus subtilis

Released:
DOI: 10.2210/pdb3mfd/pdb
PDB entry 3mfd coloured by chain, front view.
PDB entry 3mfd coloured by chain, side view.
PDB entry 3mfd coloured by chain, top view.
Source organism: Bacillus subtilis
Entry authors: Cuff ME, Rakowski E, Buck K, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152804 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase DacB Chains: A, B
Molecule details ›
Chains: A, B
Length: 334 amino acids
Theoretical weight: 38.35 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P35150 (Residues: 27-358; Coverage: 93%)
Gene names: BSU23190, dacB
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand CIT 4 x CIT
Ligand EDO 8 x EDO
1 modified residue:
Ligand MSE 28 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P43212
Unit cell:
a: 100.439Å b: 100.439Å c: 171.853Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.165 0.19
Expression system: Escherichia coli BL21(DE3)

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