2P76

Crystal structure of a Glycerophosphodiester Phosphodiesterase from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a Glycerophosphodiester Phosphodiesterase from Staphylococcus aureus

Fedorov, A.A.Fedorov, E.V.Sauder, J.M.Burley, S.K.Almo, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerophosphoryl diester phosphodiesterase
A, B, C, D, E, F, G, H
287Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: glpQ
Find proteins for A0A0H3JTK7 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  A0A0H3JTK7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.249 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.164α = 90.00
b = 115.164β = 90.00
c = 451.335γ = 120.00
Software Package:
Software NamePurpose
SHELXSphasing
ADSCdata collection
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-11-14
    Type: Data collection, Structure summary