2PZ0

Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis

Structural Biology Knowledgebase: 2PZ0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.229

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2PZ0

Classification: HYDROLASE

Total Structure Weight: 57831.35

Macromolecule Entities
Molecule Chains Length Organism Details
Glycerophosphoryl diester phosphodiesterase A, B 252 Caldanaerobacter subterraneus Gene Name(s): UgpQ TTE0993

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.229
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.40 α = 90.00
b = 53.61 β = 97.91
c = 110.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-05-17
  • Released Date: 2008-04-01
  • Deposition author(s): Shi, L., Liu, J.F., An, X.M., Liang, D.C.

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4