2P76

Crystal structure of a Glycerophosphodiester Phosphodiesterase from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb2P76/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus N315
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-20 Released: 2007-04-03 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.265 
• R-Value Work: 0.249 
• R-Value Observed: 0.249 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 8 assigned by authors.

Macromolecule Content

• Total Structure Weight: 267.39 kDa 
• Atom Count: 17,578 
• Modelled Residue Count: 2,136 
• Deposited Residue Count: 2,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphoryl diester phosphodiesterase	A, B, C, D, E, F, G, H	287	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0  Gene Names: glpQ, SA0820 EC: 3.1.4.46
UniProt
Find proteins for A0A0H3JTK7 (Staphylococcus aureus (strain N315)) Explore A0A0H3JTK7  Go to UniProtKB:  A0A0H3JTK7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.265 
• R-Value Work: 0.249 
• R-Value Observed: 0.249 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.164	α = 90
b = 115.164	β = 90
c = 451.335	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-03 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-04-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  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
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references