PDB-5ht0: Crystal structure of an Antibiotic_NAT family aminoglycoside acet...

ID or keywords:

Entry

Database: PDB / ID: 5ht0

Title

Crystal structure of an Antibiotic_NAT family aminoglycoside acetyltransferase HMB0038 from an uncultured soil metagenomic sample in complex with coenzyme A

Components

Aminoglycoside acetyltransferase HMB0005

Keywords

TRANSFERASE / Antibiotic_NAT family /

ACETYLTRANSFERASE /

AMINOGLYCOSIDE /

ANTIBIOTIC RESISTANCE /

METAGENOME / SOIL /

COENZYME A / CSGID / Center for Structural Genomics of Infectious Diseases

Function / homology

aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic /

COENZYME A / Aminoglycoside N(3)-acetyltransferase

Function and homology information

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.752 Å

Authors

Xu, Z. / Stogios, P.J. / Wawrzak, Z. / Skarina, T. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Commun Biol / Year: 2022
Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.
Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, A.

History

Deposition	Jan 26, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 6, 2022	Group: Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_oper_list Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 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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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/5ht0 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/5ht0	HTTPS FTP

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Related structure data

Related structure data	6mmzC 6mn0C 6mn3C 6mn4C 6mn5C 7kesC 7laoC 7lapC 2nygS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7kes-d 6mn0-2 6mn1-d 6mmz-3 1vfg-2 5yy5-1 6mmz-1 5wna-1 6vry-d 4m1d-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP95436

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: Aminoglycoside acetyltransferase HMB0005

B: Aminoglycoside acetyltransferase HMB0005

C: Aminoglycoside acetyltransferase HMB0005

D: Aminoglycoside acetyltransferase HMB0005

E: Aminoglycoside acetyltransferase HMB0005

F: Aminoglycoside acetyltransferase HMB0005

hetero molecules

179 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aminoglycoside acetyltransferase HMB0005

B: Aminoglycoside acetyltransferase HMB0005

hetero molecules

defined by author
59.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Aminoglycoside acetyltransferase HMB0005

D: Aminoglycoside acetyltransferase HMB0005

hetero molecules

defined by author
59.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Aminoglycoside acetyltransferase HMB0005

F: Aminoglycoside acetyltransferase HMB0005

hetero molecules

defined by author
59.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.016, 159.501, 146.225
Angle α, β, γ (deg.)	90.00, 94.74, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-305- SO4

#1: Protein	Aminoglycoside acetyltransferase HMB0005 Mass: 28753.482 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A059X981
#2: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	... ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 340 / 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: 3.61 Å³/Da / Density % sol: 65.91 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 11 Details: 2 M ammonium sulfate, 0.5 M Capso pH 11, 10mM sisomycin, 5mM coenzyme A

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.75→25 Å / % possible obs: 96.7 % / Redundancy: 4 % / R_merge(I) obs: 0.074 / Net I/σ(I): 17.76
Reflection shell	Resolution: 2.75→2.8 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 3.19 / % possible all: 90.4

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
BALBES		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2NYG

2nyg

Resolution: 2.752→24.973 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2331	2021	3.36 %	Random selection
R_work	0.2038	-	-	-
obs	0.2048	60061	95.13 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.752→24.973 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12016	0	393	340	12749

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	12694
X-RAY DIFFRACTION	f_angle_d	1.827	17304
X-RAY DIFFRACTION	f_dihedral_angle_d	16.967	4646
X-RAY DIFFRACTION	f_chiral_restr	0.066	1830
X-RAY DIFFRACTION	f_plane_restr	0.006	2228

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7525-2.8212	0.3077	121	0.3128	3197	X-RAY DIFFRACTION	74
2.8212-2.8974	0.3057	129	0.31	4022	X-RAY DIFFRACTION	92
2.8974-2.9825	0.339	153	0.2924	3977	X-RAY DIFFRACTION	92
2.9825-3.0786	0.3872	124	0.2976	4023	X-RAY DIFFRACTION	93
3.0786-3.1885	0.2714	142	0.2757	4092	X-RAY DIFFRACTION	93
3.1885-3.3158	0.2733	153	0.2458	4084	X-RAY DIFFRACTION	95
3.3158-3.4664	0.2527	141	0.2252	4199	X-RAY DIFFRACTION	97
3.4664-3.6486	0.2649	146	0.2111	4273	X-RAY DIFFRACTION	98
3.6486-3.8764	0.2013	145	0.1836	4352	X-RAY DIFFRACTION	100
3.8764-4.1744	0.1937	162	0.171	4365	X-RAY DIFFRACTION	100
4.1744-4.5922	0.1897	147	0.1541	4358	X-RAY DIFFRACTION	100
4.5922-5.2513	0.1761	151	0.154	4363	X-RAY DIFFRACTION	100
5.2513-6.5959	0.2189	151	0.1891	4368	X-RAY DIFFRACTION	100
6.5959-24.9743	0.2192	156	0.1825	4367	X-RAY DIFFRACTION	98

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	6.7709	-0.8347	0.5728	4.0082	0.3249	3.8448	-0.068	-0.1847	0.0009	-0.0043	0.1353	-0.5161	-0.0362	0.5719	-0.0357	0.2514	0.0104	0.0482	0.2145	0.0249	0.2708	117.5248	-14.9431	306.5516
2	3.1793	-2.6058	-4.5625	2.1412	3.7381	6.5493	-0.8014	-1.0749	-1.9575	2.3289	0.0371	1.555	1.3383	-0.5432	0.6462	1.5514	-0.1054	0.5415	0.8375	0.0272	1.3893	86.2763	-5.1955	310.6624
3	1.241	-0.2689	0.7135	3.3624	-0.2307	1.4066	0.0379	0.0378	0.0689	-0.0343	0.0665	0.284	0.0115	-0.0769	-0.0961	0.181	0.0432	-0.0133	0.2618	0.0086	0.2635	100.5065	-16.0418	302.1898
4	5.2364	3.2387	-3.6772	6.8742	-6.1665	6.6438	0.0734	0.2755	0.1546	-0.0222	1.0098	1.5138	0.3119	-0.724	-1.0297	0.2896	-0.0136	-0.023	0.3643	-0.0002	0.8158	86.329	-11.4739	299.5727
5	2.4462	-1.393	0.8158	4.0325	-1.5446	1.6291	0.0581	-0.5017	-0.218	0.1927	0.0675	0.4625	0.2306	-0.1899	-0.1615	0.3109	-0.0181	0.0258	0.3283	-0.0169	0.2919	100.217	-27.411	311.0479
6	2.3872	1.6877	2.1332	2.2148	0.8643	2.3087	0.2675	-0.696	0.2576	0.2531	0.1685	0.5845	-0.02	-0.8668	-0.4335	0.381	-0.0066	0.0484	0.4661	-0.009	0.2774	89.4132	11.9303	308.2432
7	7.9626	-0.2602	-0.383	2.7202	0.0517	3.7379	-0.0017	0.0155	-0.005	-0.0508	0.0478	-0.073	0.0169	-0.0547	-0.1086	0.2075	0.0109	-0.0144	0.1283	-0.044	0.2402	102.4211	12.7973	304.4606
8	3.7086	-4.955	-1.7904	7.5023	-0.2968	9.1376	-0.2736	-0.3038	2.6417	2.4105	-0.6972	0.4749	-0.4455	-0.2148	1.0117	1.2231	-0.05	-0.3744	1.1231	-0.4927	1.9664	130.6439	2.8153	315.1645
9	2.6973	-1.0879	-0.6346	2.3048	0.4917	0.5022	0.004	-0.2079	0.3213	0.1151	0.1414	-0.4017	-0.0591	0.2907	-0.1351	0.2724	-0.0364	-0.0366	0.3239	-0.0401	0.3343	120.5662	13.5876	304.4707
10	9.0989	1.5778	-0.5985	5.3267	-0.4435	4.2086	-0.0835	-0.5085	0.8123	0.1932	0.1323	-0.1662	-0.463	0.3644	0.0266	0.3148	0.0239	0.0382	0.2634	-0.0853	0.2898	110.5356	29.0673	313.779
11	7.9329	1.1782	-0.4795	8.9491	-6.2092	7.3639	-0.2009	-0.1678	0.2604	0.6104	-0.1314	-1.093	-0.7568	0.7488	0.2894	0.4412	-0.0456	-0.1164	0.5086	-0.1227	0.5163	121.9188	52.3893	332.4154
12	2.0393	1.6144	-0.3157	3.0414	0.8127	2.3817	-0.2927	0.6882	0.5696	0.1241	0.1138	0.0346	0.206	0.2953	0.3203	0.4152	0.0916	-0.1049	0.4947	0.0162	0.3282	113.9271	40.8537	331.7493
13	3.156	0.8897	-3.8553	8.3568	-5.8779	8.7646	-0.6116	-1.4902	-0.2334	0.2747	0.765	0.9344	0.3756	0.3255	-0.2973	0.5487	0.0616	-0.0008	0.6045	-0.037	0.3748	90.9239	36.4819	330.6356
14	3.0679	0.623	0.9251	2.73	-0.7541	2.8108	0.0488	-0.5359	-0.3084	0.4195	-0.0467	-0.1997	0.1343	-0.2366	0.0113	0.4546	-0.0026	-0.0287	0.4707	0.0103	0.2953	107.7183	34.797	337.6365
15	5.2105	2.3044	-1.6391	6.6232	-3.3417	7.427	0.2207	-1.1994	-0.1511	1.2856	-0.2235	-0.7074	-0.3483	0.7154	-0.0124	0.7317	0.0167	-0.2326	0.7478	-0.1122	0.4964	116.568	41.7582	353.2603
16	5.922	2.6314	4.7648	4.2586	1.1017	4.1672	0.6286	-2.3742	1.604	1.6647	-0.3265	3.2037	-1.6256	-3.5873	-0.0686	0.6809	0.0504	0.3734	1.254	-0.0382	0.9291	80.8843	47.6724	327.2356
17	6.4804	0.6255	0.359	2.9853	-0.0417	5.7386	-0.0525	-0.2783	-0.0313	0.2116	0.2809	0.1145	0.2528	0.0109	-0.2145	0.3104	0.0029	-0.0144	0.2136	-0.017	0.3199	93.3476	48.5844	314.971
18	9.1868	5.7047	-5.8321	3.5426	-3.623	3.7113	1.4569	-0.4909	-0.2997	0.7163	-0.6859	0.5042	-0.4701	-1.8739	-0.6674	1.126	0.0511	-0.1756	1.596	-0.0227	0.7863	119.6467	69.1006	319.2728
19	2.5533	-0.0331	-0.001	1.7629	-0.7403	1.2775	0.034	-0.1587	0.1104	0.053	-0.0534	-0.2478	-0.0341	0.0541	0.0331	0.2758	-0.0144	-0.0186	0.2411	-0.0395	0.2962	105.55	59.5732	307.6187
20	4.4696	3.2655	-2.459	7.2342	-5.4333	7.3846	0.0188	0.3816	0.3569	-0.0723	0.6463	0.5835	-0.0253	-0.4809	-0.8029	0.1752	-0.0109	0.0547	0.3669	-0.0007	0.4052	88.4702	64.0738	302.5919
21	4.5566	-1.8554	0.8084	5.4508	-1.7983	5.0125	-0.1629	-0.0547	-0.3086	-0.3578	0.0016	-0.2219	0.2292	0.4497	0.1332	0.3486	-0.067	0.0529	0.4247	-0.0456	0.2822	126.2623	28.5161	252.8074
22	6.0398	-1.2968	-7.4847	7.2552	0.045	9.6251	-0.5144	5.9438	-1.2328	-4.2026	-0.1105	1.4074	1.8743	-2.3155	0.6175	1.8117	-0.1814	-0.2392	2.0172	-0.1347	0.8299	94.9517	38.6557	242.0545
23	2.7124	-0.6454	-1.029	3.1578	-0.6555	1.6619	0.0162	0.4925	0.0884	-0.2505	0.1064	0.0305	-0.238	-0.1133	-0.141	0.4628	-0.0903	-0.0352	0.4677	0.003	0.2476	113.9046	42.4735	246.9408
24	5.2845	-0.6527	-2.051	9.686	6.4784	4.9149	0.5112	2.0083	-0.0643	-1.0209	-1.0349	0.6127	0.0858	-1.9931	0.7483	0.8009	-0.1857	0.0052	1.2547	0.0008	0.482	111.4255	42.6485	232.0624
25	3.4384	-1.5816	1.6272	4.7606	-3.7228	7.7577	-0.0272	0.8261	0.2016	-1.1993	-0.033	-0.793	0.1371	0.6767	-0.0071	0.8068	-0.1552	0.1644	0.8426	-0.1029	0.4223	127.5948	35.6603	231.9183
26	6.8187	-2.2159	0.3646	3.8142	-0.3465	4.0118	0.0774	0.3864	0.2449	-0.1876	-0.0069	0.1784	-0.3192	-0.1398	-0.1347	0.3142	-0.0582	0.0251	0.1712	0.0116	0.3183	96.0315	29.3903	264.5424
27	6.2862	-6.825	-5.9588	7.4323	6.4801	5.6536	0.8148	-0.026	0.0655	-1.2972	-0.6863	-0.0296	-0.3166	-0.9664	-0.2573	0.8839	0.0857	-0.0219	1.1382	-0.14	0.6151	121.5621	11.4672	267.172
28	8.4374	-2.4685	-1.0749	3.7123	-1.8547	3.8674	0.1342	0.24	-0.0522	-0.0119	-0.0585	-0.2442	-0.0894	0.3431	-0.0715	0.2272	-0.0727	-0.018	0.2771	-0.0636	0.246	114.0306	24.4115	268.9871
29	4.5729	0.203	0.92	1.9897	-0.244	1.5664	-0.0668	0.0228	-0.0519	-0.0052	0.0434	0.0035	0.014	0.0535	0.0176	0.2779	-0.0117	0.0103	0.1768	-0.0102	0.2239	103.025	14.4262	277.0487
30	5.5898	2.8715	-5.2182	4.1694	-1.3921	5.4892	0.6693	-0.0592	-1.084	-0.0795	-1.0587	0.6891	0.3208	0.4574	0.3115	0.5701	0.1066	-0.0344	0.4868	0.0559	0.4136	95.0194	-1.3792	285.494

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 4:66)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 67:74)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 75:179)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 180:193)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 194:262)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 3:14)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 15:67)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 68:74)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 75:210)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 211:262)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 3:50)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 51:67)
13	X-RAY DIFFRACTION	13	(CHAIN C AND RESID 68:88)
14	X-RAY DIFFRACTION	14	(CHAIN C AND RESID 89:206)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 207:263)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 3:6)
17	X-RAY DIFFRACTION	17	(CHAIN D AND RESID 7:69)
18	X-RAY DIFFRACTION	18	(CHAIN D AND RESID 70:75)
19	X-RAY DIFFRACTION	19	(CHAIN D AND RESID 76:227)
20	X-RAY DIFFRACTION	20	(CHAIN D AND RESID 228:262)
21	X-RAY DIFFRACTION	21	(CHAIN E AND RESID 3:68)
22	X-RAY DIFFRACTION	22	(CHAIN E AND RESID 69:75)
23	X-RAY DIFFRACTION	23	(CHAIN E AND RESID 76:199)
24	X-RAY DIFFRACTION	24	(CHAIN E AND RESID 200:210)
25	X-RAY DIFFRACTION	25	(CHAIN E AND RESID 211:263)
26	X-RAY DIFFRACTION	26	(CHAIN F AND RESID 4:66)
27	X-RAY DIFFRACTION	27	(CHAIN F AND RESID 67:72)
28	X-RAY DIFFRACTION	28	(CHAIN F AND RESID 73:129)
29	X-RAY DIFFRACTION	29	(CHAIN F AND RESID 130:256)
30	X-RAY DIFFRACTION	30	(CHAIN F AND RESID 257:262)

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