2OOG

Crystal structure of glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus

PDB DOI: 10.2210/pdb2OOG/pdb

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

Deposited: 2007-01-25 Released: 2007-02-06
Deposition Author(s): Patskovsky, Y., Fedorov, E., Toro, R., Sauder, J.M., Smith, D., Freeman, J., Maletic, M., Powell, A., Gheyi, T., Wasserman, S.R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphoryl diester phosphodiesterase	A, B, C, D, E, F A, B, C, D, E, F	287	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0 Gene Names: glpQ, SA0820 EC: 3.1.4.46
UniProt
Find proteins for A0A0H3K7S1 (Staphylococcus aureus (strain Newman)) Explore A0A0H3K7S1 Go to UniProtKB: A0A0H3K7S1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3K7S1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain DA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain R [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain R [auth B]	DA [auth C], H [auth A], HA [auth D], I [auth A], J [auth A], 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 SDF format, chain AA [auth B] SDF format, chain CB [auth F] SDF format, chain DB [auth F] SDF format, chain EB [auth F] SDF format, chain IA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain PA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth F] SDF format, chain Z [auth B] SDF format, chain AB [auth F] SDF format, chain BA [auth B] SDF format, chain BB [auth F] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain JA [auth D] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain QA [auth D] SDF format, chain SA [auth E] SDF format, chain VA [auth E] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth B] MOL2 format, chain CB [auth F] MOL2 format, chain DB [auth F] MOL2 format, chain EB [auth F] MOL2 format, chain IA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain ZA [auth F]	AA [auth B], AB [auth F], BA [auth B], BB [auth F], CB [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 SDF format, chain CA [auth C] SDF format, chain GA [auth D] SDF format, chain Q [auth B] SDF format, chain RA [auth E] SDF format, chain XA [auth F] SDF format, chain G [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain XA [auth F] MOL2 format, chain G [auth A]	CA [auth C], G [auth A], GA [auth D], Q [auth B], RA [auth E], 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 = 156.312	α = 90
b = 183.546	β = 90
c = 176.79	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-02-06

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

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