› 6gbk

X-ray diffraction
1.9Å resolution

Repertoires of functionally diverse enzymes through computational design at epistatic active-site positions

Released:
DOI: 10.2210/pdb6gbk/pdb
PDB entry 6gbk coloured by chain, front view.
PDB entry 6gbk coloured by chain, side view.
PDB entry 6gbk coloured by chain, top view.
Source organism: Brevundimonas diminuta
Primary publication:
Automated Design of Efficient and Functionally Diverse Enzyme Repertoires.
Khersonsky O, Lipsh R, Avizemer Z, Ashani Y, Goldsmith M, Leader H, Dym O, Rogotner S, Trudeau DL, Prilusky J, Amengual-Rigo P, Guallar V, Tawfik DS, Fleishman SJ
Mol Cell 72 178-186.e5 (2018)
PMID: 30270109

Function and Biology Details

Reaction catalysed: 
An aryl dialkyl phosphate + H(2)O = dialkyl phosphate + an aryl alcohol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141251 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Parathion hydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 335 amino acids
Theoretical weight: 36.47 KDa
Source organism: Brevundimonas diminuta
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A434 (Residues: 34-365; Coverage: 99%)
Gene name: opd
Sequence domains: Phosphotriesterase family
Structure domains: Metal-dependent hydrolases

Ligands and Environments

3 bound ligands:
Ligand FMT 2 x FMT
Ligand ZN 4 x ZN
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: C2
Unit cell:
a: 156.749Å b: 53.09Å c: 89.23Å
α: 90° β: 106.81° γ: 90°
R-values:
R R work R free
0.184 0.182 0.212
Expression system: Escherichia coli

Quick links

Citations

25 review citations

Harnessing Conformational Plasticity to Generate Designer Enzymes.
Crean et al. (2020)
24 more

1 mention without citation

Automated Design of Efficient and Functionally Diverse Enzyme Repertoires.
Khersonsky et al. (2018)