2OOG | pdb_00002oog

Crystal structure of glycerophosphoryl diester phosphodiesterase from Staphylococcus aureus

PDB DOI: https://doi.org/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 (Depositor), 0.277 (DCC)
R-Value Work:
0.235 (Depositor), 0.231 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 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.

Macromolecule Content

Total Structure Weight: 204.41 kDa
Atom Count: 14,474
Modeled Residue Count: 1,603
Deposited Residue Count: 1,722
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphoryl diester phosphodiesterase	A, B, C, D, E 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3K7S1
Sequence Annotations 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 DA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF 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		Interactions Focus chain DA [auth C] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain DA [auth C] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth F] SDF format, chain BA [auth B] SDF format, chain BB [auth F] SDF format, chain CB [auth F] SDF format, chain DB [auth F] SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain FA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [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 M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth E] 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 VA [auth E] 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 ZA [auth F] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [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 M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] 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 VA [auth E] 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 ZA [auth F] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth F] mmCIF format, chain CB [auth F] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth B] mmCIF 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		Interactions Focus chain AA [auth B] Focus chain AB [auth F] Focus chain BA [auth B] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth F] Focus chain BA [auth B] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Focus chain ZA [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain Q [auth B] SDF format, chain RA [auth E] SDF format, chain XA [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain XA [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain XA [auth F]	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		Interactions Focus chain CA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain Q [auth B] Focus chain RA [auth E] Focus chain XA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain Q [auth B] Focus chain RA [auth E] Focus chain XA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.280 (Depositor), 0.277 (DCC)
R-Value Work: 0.235 (Depositor), 0.231 (DCC)
R-Value Observed: 0.236 (Depositor)

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

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View more in-depth experimental data

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
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Refinement description