› 2rb5

X-ray diffraction
1.03Å resolution

X-ray Crystallographic Structures Show Conservation of a Trigonal-Bipyramidal Intermediate in a Phosphoryl-transfer Superfamily.

Released:
DOI: 10.2210/pdb2rb5/pdb
PDB entry 2rb5 coloured by chain, front view.
PDB entry 2rb5 coloured by chain, side view.
PDB entry 2rb5 coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron VPI-5482
Primary publication:
The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state.
Lu Z, Dunaway-Mariano D, Allen KN
Proc Natl Acad Sci U S A 105 5687-92 (2008)
PMID: 18398008

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183592 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Haloacid dehalogenase-like hydrolase Chain: A
Molecule details ›
Chain: A
Length: 261 amino acids
Theoretical weight: 28.89 KDa
Source organism: Bacteroides thetaiotaomicron VPI-5482
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8A090 (Residues: 1-261; Coverage: 100%)
Gene name: BT_4131
Sequence domains: haloacid dehalogenase-like hydrolase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand WO6 1 x WO6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P212121
Unit cell:
a: 49.387Å b: 56.467Å c: 94.447Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.112 0.11 0.136
Expression system: Escherichia coli

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Citations

4 review citations

Serine/threonine phosphatases: mechanism through structure.
Shi Y. (2009)
3 more

3 mentions without citation

The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state.
Lu et al. (2008)
2 more