1k2x

X-ray diffraction
1.65Å resolution

Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene

Released:
Source organism: Escherichia coli
Primary publication:
Crystal packing of plant-type L-asparaginase from Escherichia coli.
Acta Crystallogr D Biol Crystallogr 64 309-20 (2008)
PMID: 18323626

Function and Biology Details

Reaction catalysed:
Cleavage of a beta-linked Asp residue from the N-terminus of a polypeptide.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-153446 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Isoaspartyl peptidase subunit alpha Chains: A, C
Molecule details ›
Chains: A, C
Length: 177 amino acids
Theoretical weight: 18.96 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P37595 (Residues: 2-178; Coverage: 55%)
Gene names: JW0812, b0828, iaaA, spt, ybiK
Sequence domains: Asparaginase
Isoaspartyl peptidase subunit beta Chains: B, D
Molecule details ›
Chains: B, D
Length: 143 amino acids
Theoretical weight: 14.43 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P37595 (Residues: 179-321; Coverage: 45%)
Gene names: JW0812, b0828, iaaA, spt, ybiK
Sequence domains: Asparaginase
Structure domains: (Glycosyl)asparaginase

Ligands and Environments

2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X31
Spacegroup: P212121
Unit cell:
a: 50.296Å b: 77.624Å c: 148.152Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.163 0.198
Expression system: Escherichia coli