› 3r5f

X-ray diffraction
2.07Å resolution

Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with ATP

Released:
DOI: 10.2210/pdb3r5f/pdb
PDB entry 3r5f coloured by chain, front view.
PDB entry 3r5f coloured by chain, side view.
PDB entry 3r5f coloured by chain, top view.
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Entry authors: Doan TTN, Kim JK, Kang LW

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-177168 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chain: A
Molecule details ›
Chain: A
Length: 384 amino acids
Theoretical weight: 41.76 KDa
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5H614 (Residues: 1-347; Coverage: 100%)
Gene names: XOO0352, ddl, ddlA
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: P43212
Unit cell:
a: 83.225Å b: 83.225Å c: 97.143Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.208 0.277
Expression system: Escherichia coli

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