› 5z01

X-ray diffraction
1.75Å resolution

Native Escherichia coli L,D-carboxypeptidase A (LdcA)

Released:
DOI: 10.2210/pdb5z01/pdb
PDB entry 5z01 coloured by chain, front view.
PDB entry 5z01 coloured by chain, side view.
PDB entry 5z01 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The crystal structure and oligomeric form of Escherichia colil,d-carboxypeptidase A.
Meyer K, Addy C, Akashi S, Roper DI, Tame JRH
Biochem Biophys Res Commun 499 594-599 (2018)
PMID: 29601819

Function and Biology Details

Reaction catalysed: 
GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H(2)O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160029 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Murein tetrapeptide carboxypeptidase Chain: A
Molecule details ›
Chain: A
Length: 323 amino acids
Theoretical weight: 35.69 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P76008 (Residues: 1-304; Coverage: 100%)
Gene names: JW1181, b1192, ldcA, ycgQ
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: I222
Unit cell:
a: 77.949Å b: 89.069Å c: 93.772Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.176 0.225
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Cell-Wall Recycling of the Gram-Negative Bacteria and the Nexus to Antibiotic Resistance.
Dik et al. (2018)
1 other article