› 2efu

X-ray diffraction
2.3Å resolution

The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine

Released:
DOI: 10.2210/pdb2efu/pdb
PDB entry 2efu coloured by chain, front view.
PDB entry 2efu coloured by chain, side view.
PDB entry 2efu coloured by chain, top view.
Source organism: Brucella anthropi
Primary publication:
Structures of D-amino-acid amidase complexed with L-phenylalanine and with L-phenylalanine amide: insight into the D-stereospecificity of D-amino-acid amidase from Ochrobactrum anthropi SV3.
Okazaki S, Suzuki A, Mizushima T, Komeda H, Asano Y, Yamane T
Acta Crystallogr D Biol Crystallogr 64 331-4 (2008)
PMID: 18323628

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192256 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-lactamase-related domain-containing protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 363 amino acids
Theoretical weight: 40.13 KDa
Source organism: Brucella anthropi
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9LCC8 (Residues: 1-363; Coverage: 100%)
Gene name: daaA
Sequence domains: Beta-lactamase
Structure domains: DD-peptidase/beta-lactamase superfamily

Ligands and Environments

2 bound ligands:
Ligand BA 25 x BA
Ligand PHE 6 x PHE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P21
Unit cell:
a: 77.468Å b: 123.274Å c: 116.156Å
α: 90° β: 104.05° γ: 90°
R-values:
R R work R free
0.174 0.17 0.235
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Distribution, industrial applications, and enzymatic synthesis of D-amino acids.
Gao et al. (2015)
3 other articles

3 mentions without citation

Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins.
Fedosyuk et al. (2016)
2 more