› 3l12

X-ray diffraction
1.6Å resolution

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (YP_165505.1) from Silicibacter pomeroyi DSS-3 at 1.60 A resolution

Released:
DOI: 10.2210/pdb3l12/pdb
PDB entry 3l12 coloured by chain, front view.
PDB entry 3l12 coloured by chain, side view.
PDB entry 3l12 coloured by chain, top view.
Source organism: Ruegeria pomeroyi
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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177577 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GP-PDE domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 313 amino acids
Theoretical weight: 34.88 KDa
Source organism: Ruegeria pomeroyi
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5LX22 (Residues: 1-312; Coverage: 100%)
Gene name: SPO0236
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

3 bound ligands:
Ligand MG 3 x MG
Ligand CL 5 x CL
Ligand UNL 2 x UNL
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P21
Unit cell:
a: 50.409Å b: 136.411Å c: 50.548Å
α: 90° β: 118° γ: 90°
R-values:
R R work R free
0.158 0.156 0.187
Expression system: Escherichia coli

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