2OOG

Crystal structure of glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase from Staphylococcus Aureus

Patskovsky, Y.Sauder, J.M.Smith, D.Freeman, J.Maletic, M.Powell, A.Gheyi, T.Wasserman, S.R.Burley, S.K.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycerophosphoryl diester phosphodiesteraseA, B, C, D, E, F287Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: glpQSA0820
EC: 3.1.4.46
UniProt
Find proteins for A0A0H3K7S1 (Staphylococcus aureus (strain Newman))
Explore A0A0H3K7S1 
Go to UniProtKB:  A0A0H3K7S1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth C], H [auth A], HA [auth D], I [auth A], J [auth A], R [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B] , AB [auth F] , BA [auth B] , BB [auth F] , CB [auth F] , DB [auth F] , EA [auth C] , EB [auth F] , 
AA [auth B], AB [auth F], BA [auth B], BB [auth F], CB [auth F], DB [auth F], EA [auth C], EB [auth F], FA [auth C], IA [auth D], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], QA [auth D], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B], Y [auth B], YA [auth F], Z [auth B], ZA [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth C], G [auth A], GA [auth D], Q [auth B], RA [auth E], XA [auth F]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.312α = 90
b = 183.546β = 90
c = 176.79γ = 90
Software Package:
Software NamePurpose
PHASERphasing
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2007-11-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-11-14
    Changes: Data collection, Structure summary
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary