5V0Z | pdb_00005v0z

Crystal structure of Galactoside O-acetyltransferase complex with CoA (P32 space group).

PDB DOI: https://doi.org/10.2210/pdb5V0Z/pdb

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

Deposited: 2017-02-28 Released: 2017-03-15
Deposition Author(s): Czub, M.P., Porebski, P.J., Knapik, A.A., Niedzialkowska, E., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free:
0.164 (Depositor), 0.197 (DCC)
R-Value Work:
0.136 (Depositor)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Galactoside O-acetyltransferase complex with CoA (P32 space group).

Czub, M.P., Porebski, P.J., Knapik, A.A., Niedzialkowska, E., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 70.27 kDa
Atom Count: 5,762
Modeled Residue Count: 567
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetyltransferase SACOL2570	A, B, C	202	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: SACOL2570 EC: 2.3.1
UniProt
Find proteins for Q5HCZ5 (Staphylococcus aureus (strain COL)) Explore Q5HCZ5 Go to UniProtKB: Q5HCZ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HCZ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain I [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain I [auth A]	I [auth A], X [auth B], Y [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain I [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain I [auth A] Focus chain X [auth B] Focus chain Y [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain LA [auth C] SDF format, chain F [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain F [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain F [auth A]	F [auth A], LA [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain LA [auth C] Interactions & Density Focus chain F [auth A] Focus chain LA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain KA [auth C] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], KA [auth C], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain KA [auth C] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain KA [auth C] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] MA [auth C] NA [auth C] V [auth B] G [auth A], H [auth A], MA [auth C], NA [auth C], V [auth B], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain V [auth B] Focus chain W [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RA [auth C] SDF format, chain R [auth A] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], Z [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.164 (Depositor), 0.197 (DCC)
R-Value Work: 0.136 (Depositor)
R-Value Observed: 0.138 (Depositor)

Diffraction Data:

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.434	α = 90
b = 75.434	β = 90
c = 93.178	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-03-15
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description