› 3no3

X-ray diffraction
1.89Å resolution

Crystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution

Released:
DOI: 10.2210/pdb3no3/pdb
PDB entry 3no3 coloured by chain, front view.
PDB entry 3no3 coloured by chain, side view.
PDB entry 3no3 coloured by chain, top view.
Source organism: Parabacteroides distasonis ATCC 8503
Entry author: Joint Center for Structural Genomics (JCSG)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107908 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GP-PDE domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 238 amino acids
Theoretical weight: 27.83 KDa
Source organism: Parabacteroides distasonis ATCC 8503
Expression system: Escherichia coli
UniProt:
  • Canonical: A6L916 (Residues: 22-258; Coverage: 100%)
Gene name: BDI_0402
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand GOL 1 x GOL
Ligand PEG 1 x PEG
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2
Unit cell:
a: 137.46Å b: 40.876Å c: 48.328Å
α: 90° β: 99.39° γ: 90°
R-values:
R R work R free
0.151 0.15 0.177
Expression system: Escherichia coli

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