› 2zma

X-ray diffraction
1.51Å resolution

Crystal Structure of 6-Aminohexanoate-dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate

Released:
DOI: 10.2210/pdb2zma/pdb
PDB entry 2zma coloured by chain, front view.
PDB entry 2zma coloured by chain, side view.
PDB entry 2zma coloured by chain, top view.
Source organism: Paenarthrobacter ureafaciens
Primary publication:
Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold.
Kawashima Y, Ohki T, Shibata N, Higuchi Y, Wakitani Y, Matsuura Y, Nakata Y, Takeo M, Kato D, Negoro S
FEBS J 276 2547-56 (2009)
PMID: 19476493

Function and Biology Details

Reaction catalysed: 
(N-(6-aminohexanoyl))(n) + H(2)O = (N-(6-aminohexanoyl))(n-1) + 6-aminohexanoate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139359 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6-aminohexanoate-dimer hydrolase Chain: A
Molecule details ›
Chain: A
Length: 392 amino acids
Theoretical weight: 42.91 KDa
Source organism: Paenarthrobacter ureafaciens
Expression system: Escherichia coli
UniProt:
  • Canonical: P07061 (Residues: 1-28, 181-208, 266-296; Coverage: 22%)
  • Canonical: P07062 (Residues: 29-180, 209-265, 297-392; Coverage: 78%)
Gene names: nylB, nylB'
Sequence domains: Beta-lactamase
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand SO4 5 x SO4
Ligand ACA 2 x ACA
Ligand MES 1 x MES
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P3221
Unit cell:
a: 96.687Å b: 96.687Å c: 112.911Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.175 0.19
Expression system: Escherichia coli

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Citations

8 citation in other articles

Simple, yet powerful methodologies for conformational sampling of proteins.
Harada et al. (2015)
7 more