› 3mz2

X-ray diffraction
1.55Å resolution

Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution

Released:
DOI: 10.2210/pdb3mz2/pdb
PDB entry 3mz2 coloured by chain, front view.
PDB entry 3mz2 coloured by chain, side view.
PDB entry 3mz2 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:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107969 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GP-PDE domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 292 amino acids
Theoretical weight: 33.78 KDa
Source organism: Parabacteroides distasonis ATCC 8503
Expression system: Escherichia coli
UniProt:
  • Canonical: A6LIT8 (Residues: 26-316; Coverage: 99%)
Gene name: BDI_3922
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

4 bound ligands:
Ligand SO4 12 x SO4
Ligand PG4 9 x PG4
Ligand NA 1 x NA
Ligand PE4 1 x PE4
1 modified residue:
Ligand MSE 22 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P21
Unit cell:
a: 53.577Å b: 90.481Å c: 60.373Å
α: 90° β: 111.95° γ: 90°
R-values:
R R work R free
0.167 0.166 0.197
Expression system: Escherichia coli

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