› 8p7t

X-ray diffraction
1.8Å resolution

The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes

Released:
DOI: 10.2210/pdb8p7t/pdb
PDB entry 8p7t coloured by chain, front view.
PDB entry 8p7t coloured by chain, side view.
PDB entry 8p7t coloured by chain, top view.
Source organism: Brevundimonas diminuta
Primary publication:
The impact of molecular variants, crystallization conditions and the space group on ligand-protein complexes: a case study on bacterial phosphotriesterase.
Dym O, Aggarwal N, Ashani Y, Leader H, Albeck S, Unger T, Hamer-Rogotner S, Silman I, Tawfik DS, Sussman JL
OpenAccess logo Acta Crystallogr D Struct Biol (2023)
PMID: 37860961

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-531739 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Parathion hydrolase Chain: A
Molecule details ›
Chain: A
Length: 332 amino acids
Theoretical weight: 35.81 KDa
Source organism: Brevundimonas diminuta
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A434 (Residues: 34-365; Coverage: 99%)
Gene name: opd
Sequence domains: Phosphotriesterase family

Ligands and Environments

6 bound ligands:
Ligand FMT 1 x FMT
Ligand ZN 2 x ZN
Ligand VX 2 x VX
Ligand E8N 1 x E8N
Ligand GOL 6 x GOL
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P43212
Unit cell:
a: 69.45Å b: 69.45Å c: 186.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.159 0.184
Expression system: Escherichia coli

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