› 3v4z

X-ray diffraction
2.69Å resolution

D-alanine--D-alanine ligase from Yersinia pestis

Released:
DOI: 10.2210/pdb3v4z/pdb
PDB entry 3v4z coloured by chain, front view.
PDB entry 3v4z coloured by chain, side view.
PDB entry 3v4z coloured by chain, top view.
Source organism: Yersinia pestis CO92
Entry authors: Osipiuk J, Nocek B, Mulligan R, Papazisi L, Anderson WF, Joachimiak A, Center for Structural Genomics of Infectious Diseases (CSGID)

Function and Biology Details

Reaction catalysed: 
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-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-187209 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 309 amino acids
Theoretical weight: 33.45 KDa
Source organism: Yersinia pestis CO92
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8ZIE7 (Residues: 1-306; Coverage: 100%)
Gene names: YPO0557, YP_3627, ddl, ddlB, y3624
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PEG 1 x PEG
Ligand PGE 1 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P3121
Unit cell:
a: 100.637Å b: 100.637Å c: 110.304Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.205 0.289
Expression system: Escherichia coli

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