› 1ybq

X-ray diffraction
2Å resolution

Crystal structure of Escherichia coli isoaspartyl dipeptidase mutant D285N complexed with beta-aspartylhistidine

Released:
DOI: 10.2210/pdb1ybq/pdb
PDB entry 1ybq coloured by chain, front view.
PDB entry 1ybq coloured by chain, side view.
PDB entry 1ybq coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli.
Martí-Arbona R, Fresquet V, Thoden JB, Davis ML, Holden HM, Raushel FM
Biochemistry 44 7115-24 (2005)
PMID: 15882050

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153877 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Isoaspartyl dipeptidase Chain: A
Molecule details ›
Chain: A
Length: 390 amino acids
Theoretical weight: 41.12 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P39377 (Residues: 1-390; Coverage: 100%)
Gene names: JW4291, b4328, iadA, yjiF
Sequence domains: Amidohydrolase family
Structure domains:
Isoaspartyl dipeptidase Chain: B
Molecule details ›
Chain: B
Length: 390 amino acids
Theoretical weight: 41.17 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P39377 (Residues: 1-390; Coverage: 100%)
Gene names: JW4291, b4328, iadA, yjiF
Sequence domains: Amidohydrolase family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand BDH 2 x BDH
1 modified residue:
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P4212
Unit cell:
a: 119.3Å b: 119.3Å c: 138.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.181 0.243
Expression system: Escherichia coli

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Citations

19 citation in other articles

Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis.
Liu et al. (2005)
18 more

6 mentions without citation

Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily.
Xiang et al. (2009)
5 more