› 2fb9

X-ray diffraction
1.9Å resolution

Crystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes

Released:
DOI: 10.2210/pdb2fb9/pdb
PDB entry 2fb9 coloured by chain, front view.
PDB entry 2fb9 coloured by chain, side view.
PDB entry 2fb9 coloured by chain, top view.
Source organism: Thermus caldophilus
Primary publication:
Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes.
Lee JH, Na Y, Song HE, Kim D, Park BH, Rho SH, Im YJ, Kim MK, Kang GB, Lee DS, Eom SH
Proteins 64 1078-82 (2006)
PMID: 16779845

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-174808 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chain: A
Molecule details ›
Chain: A
Length: 322 amino acids
Theoretical weight: 35.11 KDa
Source organism: Thermus caldophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q3T920 (Residues: 1-319; Coverage: 100%)
Gene name: ddl
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6B
Spacegroup: C2221
Unit cell:
a: 115.216Å b: 132.744Å c: 59.324Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.249 0.228 0.268
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Cytoplasmic steps of peptidoglycan biosynthesis.
Barreteau et al. (2008)
8 other articles

2 mentions without citation

PSCDB: a database for protein structural change upon ligand binding.
Amemiya et al. (2012)
1 more