› 3byc

Hybrid

Joint neutron and X-ray structure of diisopropyl fluorophosphatase. Deuterium occupancies are 1-Q, where Q is occupancy of H

Released:
DOI: 10.2210/pdb3byc/pdb
PDB entry 3byc coloured by chain, front view.
PDB entry 3byc coloured by chain, side view.
PDB entry 3byc coloured by chain, top view.
Source organism: Loligo vulgaris
Primary publication:
Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.
Blum MM, Mustyakimov M, Rüterjans H, Kehe K, Schoenborn BP, Langan P, Chen JC
Proc Natl Acad Sci U S A 106 713-8 (2009)
PMID: 19136630

Function and Biology Details

Reaction catalysed: 
Diisopropyl fluorophosphate + H(2)O = diisopropyl phosphate + fluoride
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181980 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diisopropyl-fluorophosphatase Chain: A
Molecule details ›
Chain: A
Length: 314 amino acids
Theoretical weight: 35.12 KDa
Source organism: Loligo vulgaris
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7SIG4 (Residues: 1-314; Coverage: 100%)
Sequence domains: SMP-30/Gluconolactonase/LRE-like region
Structure domains: TolB, C-terminal domain

Ligands and Environments

2 bound ligands:
Ligand CA 2 x CA
Ligand DOD 246 x DOD
No modified residues

Experiments and Validation Details

Experimental Method: Neutron Diffraction, X-ray diffraction
X-ray source: null, RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 43.441Å b: 83.291Å c: 87.509Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.264 0.233 0.315
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Catalytic mechanisms for phosphotriesterases.
Bigley et al. (2013)
4 more

14 mentions without citation

Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography.
Chen et al. (2017)
13 more