2OTD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.221

Literature

Macromolecules
Sequence Display for 2OTD

Classification: HYDROLASE

Total Structure Weight: 111086.65

Macromolecule Entities
Molecule Chains Length Organism Details
Glycerophosphodiester phosphodiesterase A, B, C, D 247 Shigella flexneri EC#: 3.1.4.1 IUBMB
Mutation: M1M, M37M, M109M, M110M, M128M, M140M, M201M
Gene Name(s): ugpQ S4296 SF3466 NCTC1_03748
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A, B, C, D PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.221
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 80.62 α = 90.00
b = 82.18 β = 90.00
c = 223.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-07
  • Released Date: 2007-03-06
  • Deposition author(s): Zhang, R., Wu, R., Clancy, S., Jiang, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2007-03-06

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Version format compliance