PDB-3v4e: Crystal Structure of the galactoside O-acetyltransferase in compl...

ID or keywords:

Entry

Database: PDB / ID: 3v4e

Title

Crystal Structure of the galactoside O-acetyltransferase in complex with CoA

Components

Galactoside O-acetyltransferase

Keywords

TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / galactoside O-acetyltransferase / CoA

Function / homology

Function and homology information

galactoside O-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function

Biological species

Staphylococcus aureus subsp. aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Knapik, A.A. / Shumilin, I.A. / Luo, H.-B. / Chruszcz, M. / Zimmerman, M.D. / Cymborowski, M. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: J.Struct.Funct.Genom. / Year: 2013
Title: Biophysical analysis of the putative acetyltransferase SACOL2570 from methicillin-resistant Staphylococcus aureus.
Authors: Luo, H.B. / Knapik, A.A. / Petkowski, J.J. / Demas, M. / Shumilin, I.A. / Zheng, H. / Chruszcz, M. / Minor, W.

History

Deposition	Dec 14, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 15, 2017	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Sep 13, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3v4e.cif.gz	237.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3v4e.ent.gz	191.6 KB	Display	PDB format
PDBx/mmJSON format	3v4e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3v4e_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	3v4e_full_validation.pdf.gz	1.2 MB	Display
Data in XML	3v4e_validation.xml.gz	26.9 KB	Display
Data in CIF	3v4e_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v4/3v4e ftp://data.pdbj.org/pub/pdb/validation_reports/v4/3v4e	HTTPS FTP

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Related structure data

Related structure data	3fttSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ic7-d 5v0z-d 2p2o-2 5u2k-1 3ol9-3 4isx-2 5f8m-d 1e70-d 3srt-1 2p2o-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (9) #39 - Mar 2003 lac Repressor similarity (8) #49 - Jan 2004 Carbonic Anhydrase similarity (4) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Galactoside O-acetyltransferase

B: Galactoside O-acetyltransferase

C: Galactoside O-acetyltransferase

hetero molecules

69.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.424, 53.461, 53.477
Angle α, β, γ (deg.)	89.75, 89.78, 89.94
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 3 molecules ABC

#1: Protein	Galactoside O-acetyltransferase / Acetyltransferase SACOL2570 Mass: 22417.127 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: COL / Gene: SACOL2570 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3RIL References: UniProt: Q5HCZ5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

#1: Protein

Galactoside O-acetyltransferase / Acetyltransferase SACOL2570

Mass: 22417.127 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: SACOL2570 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21DE3RIL
References: UniProt: Q5HCZ5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 206 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M NA DIH PHOSPHATE, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2009
Radiation	Monochromator: C (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. all: 39809 / Num. obs: 39809 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / B_iso Wilson estimate: 26.2 Å² / R_merge(I) obs: 0.034 / R_sym value: 0.034 / Net I/σ(I): 32.7
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.075 / Mean I/σ(I) obs: 10.6 / Num. unique all: 1293 / R_sym value: 0.075 / % possible all: 57.2

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Processing

Software

Name	Version	Classification
MD2		data collection
HKL-3000		phasing
MOLREP		phasing
REFMAC	5.6.0117	refinement
Coot		model building
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3FTT

3ftt

Resolution: 1.95→50 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.908 / SU B: 6.441 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.185 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22215	2000	5 %	RANDOM
R_work	0.18039	-	-	-
all	0.18252	37809	-	-
obs	0.18252	37809	92.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 34.888 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.36 Å²	-0.39 Å²	1.34 Å²
2-	-	0.09 Å²	-0.01 Å²
3-	-	-	0.26 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4390	0	166	200	4756

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.02	4677
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	3063
X-RAY DIFFRACTION	r_angle_refined_deg	1.825	1.965	6371
X-RAY DIFFRACTION	r_angle_other_deg	1.29	3	7476
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.649	5	563
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.573	24.771	218
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.188	15	709
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.651	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	683
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	5190
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	955
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.228	78	-
R_work	0.164	1727	-
obs	-	-	56.57 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	51.396	-0.4381	-0.5356	15.7503	6.7256	2.8743	0.2324	-0.6889	-1.1956	1.0103	-0.4388	0.4095	0.43	-0.1921	0.2064	0.2273	-0.0117	0.0457	0.1383	0.1152	0.1451	-9.066	-20.033	22.931
2	2.0372	-0.8179	2.873	2.0243	-1.1061	6.6206	0.0446	0.0826	-0.1859	0.0355	-0.044	0.0692	0.4503	0.2404	-0.0007	0.0854	0.0136	0.0118	0.0623	0.058	0.1081	-6.984	-18.154	15.045
3	2.2083	-0.8458	-1.3102	0.4292	0.0338	6.1454	0.0023	0.2286	-0.1374	0.0089	-0.0246	0.0603	0.0306	-0.498	0.0223	0.0253	0.0029	-0.0473	0.0946	0.0045	0.1116	-19.373	-8.652	-2.775
4	1.1468	-0.3732	0.0603	0.7929	-0.0724	0.3838	-0.0443	-0.0791	-0.1133	0.0385	0.0071	0.067	0.0244	-0.1154	0.0372	0.0612	0.0179	-0.0218	0.0956	0.0239	0.0761	-9.233	-5.01	10.077
5	1.6914	-0.8952	-0.2245	1.1212	-0.217	0.5531	-0.0343	-0.1915	-0.0196	0.1349	0.0394	-0.0182	-0.0845	-0.0071	-0.005	0.0971	0.0261	-0.0439	0.107	0.0165	0.0354	-4.471	5.136	15.328
6	58.49	-15.5389	1.4684	8.7952	-1.5926	4.5102	0.1778	-1.4571	2.0231	0.2174	-0.0398	-0.3921	-0.6361	0.0486	-0.1381	0.2391	0.0226	-0.0136	0.0979	-0.0768	0.0971	-6.625	19.46	17.029
7	3.0045	1.9546	-0.1609	6.8611	-2.0437	7.642	-0.1167	0.1145	0.5535	-0.2645	0.2072	0.2483	-0.0689	-0.2984	-0.0905	0.0939	0.0847	-0.0316	0.1329	0.0247	0.1306	-16.967	22.658	-6.444
8	3.1287	-5.2536	-2.5375	11.4789	3.9786	2.089	-0.2816	0.2103	-0.439	0.5757	-0.0477	0.9832	0.2261	-0.1925	0.3293	0.119	0.0388	-0.0137	0.1668	0.0178	0.1564	-19.364	9.25	-9.411
9	0.6802	0.3892	-0.2985	0.8611	0.332	0.9484	-0.0311	0.0692	-0.0677	-0.1873	0.0519	-0.0227	-0.0504	-0.1396	-0.0208	0.1643	0.0213	-0.0466	0.1277	0.0256	0.0417	-5.727	2.889	-18.527
10	1.9058	-0.3016	-0.3364	0.5177	0.0279	0.4935	-0.0091	0.0144	-0.0285	-0.1164	0.0491	0.0269	-0.0665	-0.1067	-0.04	0.1078	0.0373	-0.0397	0.0732	0.0145	0.0519	-1.079	9.291	-8.863
11	1.7669	0.2274	-1.0035	0.3103	-0.1311	1.4004	0.0756	0.0846	0.1583	-0.0496	-0.0094	-0.0114	-0.2187	-0.125	-0.0662	0.1268	0.0422	-0.0337	0.0377	0.0119	0.0527	-1.851	15.383	-1.57
12	1.579	0.041	-0.2569	1.0843	0.3173	3.1762	-0.0307	-0.115	0.2247	-0.0599	0.0868	-0.1648	-0.2766	0.2983	-0.0561	0.1024	-0.0265	-0.0347	0.0528	0.0026	0.1319	15.256	16.817	-4.672
13	10.7193	3.0542	2.0065	3.6123	1.2785	4.8689	0.0746	0.4124	-0.2172	-0.1691	0.0417	-0.0299	-0.0477	0.4538	-0.1163	0.1337	0.0635	0.0244	0.0843	0.0002	0.0176	20.251	-6.243	-18.893
14	3.8294	0.0848	0.0482	0.7199	-0.0903	0.0133	-0.0582	0.2091	-0.2932	-0.261	0.075	0.1282	0.039	-0.0024	-0.0168	0.1584	0.0155	-0.0425	0.0505	-0.009	0.0804	0.454	-17.097	-11.297
15	0.6693	0.5914	-0.2344	1.2441	0.4846	1.9748	-0.0085	0.0033	-0.1763	-0.1276	-0.0807	-0.1326	0.1052	-0.0505	0.0892	0.0997	0.0396	-0.0319	0.0262	-0.0047	0.1055	8.081	-17.243	-4.988
16	2.933	-0.8112	-4.0091	2.1199	-1.3128	8.6385	0.248	0.0902	-0.0693	-0.0346	-0.0984	0.1313	-0.375	-0.0596	-0.1496	0.0752	0.0097	-0.0413	0.056	0.0227	0.1493	5.751	-9.881	-2.112
17	0.3974	-0.0689	0.1526	1.0272	-0.5405	0.9177	0.0117	-0.0614	-0.0582	-0.0964	-0.041	-0.1783	0.0398	0.0986	0.0293	0.0687	0.026	-0.0233	0.0654	0.0186	0.0944	14.651	-3.728	0.509
18	2.5159	-1.1079	-0.406	55.1466	-14.596	8.4395	-0.3143	-0.5152	0.0389	1.8329	0.4687	-1.0971	-0.3738	-0.0644	-0.1544	0.1468	0.0755	-0.0922	0.2589	0.0387	0.1272	16.78	-6.752	19.414

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 6
2	X-RAY DIFFRACTION	2	A	7 - 29
3	X-RAY DIFFRACTION	3	A	30 - 53
4	X-RAY DIFFRACTION	4	A	54 - 124
5	X-RAY DIFFRACTION	5	A	125 - 178
6	X-RAY DIFFRACTION	6	A	179 - 188
7	X-RAY DIFFRACTION	7	B	1 - 14
8	X-RAY DIFFRACTION	8	B	15 - 32
9	X-RAY DIFFRACTION	9	B	33 - 82
10	X-RAY DIFFRACTION	10	B	83 - 114
11	X-RAY DIFFRACTION	11	B	115 - 165
12	X-RAY DIFFRACTION	12	B	166 - 188
13	X-RAY DIFFRACTION	13	C	1 - 20
14	X-RAY DIFFRACTION	14	C	21 - 52
15	X-RAY DIFFRACTION	15	C	53 - 81
16	X-RAY DIFFRACTION	16	C	82 - 92
17	X-RAY DIFFRACTION	17	C	93 - 178
18	X-RAY DIFFRACTION	18	C	179 - 188

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