› 2otd

X-ray diffraction
2.6Å resolution

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a

Released:
DOI: 10.2210/pdb2otd/pdb
PDB entry 2otd coloured by chain, front view.
PDB entry 2otd coloured by chain, side view.
PDB entry 2otd coloured by chain, top view.
Source organism: Shigella flexneri
Entry authors: Zhang R, Wu R, Clancy S, Jiang S, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

Reaction catalysed: 
Hydrolytically removes 5'-nucleotides successively from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101525 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GP-PDE domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 247 amino acids
Theoretical weight: 27.68 KDa
Source organism: Shigella flexneri
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: A0A0H2V2B5 (Residues: 1-247; Coverage: 100%)
Gene names: SF3466, ugpQ
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

1 bound ligand:
Ligand PO4 4 x PO4
1 modified residue:
Ligand MSE 28 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 80.617Å b: 82.185Å c: 223.202Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.224 0.221 0.276
Expression system: Escherichia coli BL21

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