PDB-5hmn: Crystal structure of an aminoglycoside acetyltransferase HMB0005 ...

ID or keywords:

Entry

Database: PDB / ID: 5hmn

Title

Crystal structure of an aminoglycoside acetyltransferase HMB0005 from an uncultured soil metagenomic sample, unknown active site density modeled as polyethylene glycol

Components

AAC3-I

Keywords

TRANSFERASE / GNAT FOLD / GCN5-N-ACETYLTRANSFERASE FOLD / ACETYLTRANSFERASE / AMINOGLYCOSIDE / ANTIBIOTIC RESISTANCE / METAGENOME / SOIL / COENZYME A / STRUCTURAL GENOMICS / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.018 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: To Be Published
Title: Crystal structure of an aminoglycoside acetyltransferase HMB0005 from an uncultured soil metagenomic sample, unknown active site density modeled as polyethylene glycol
Authors: Xu, Z.

History

Deposition	Jan 16, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 17, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hmn.cif.gz	406 KB	Display	PDBx/mmCIF format
PDB format	pdb5hmn.ent.gz	337.9 KB	Display	PDB format
PDBx/mmJSON format	5hmn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hmn_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	5hmn_full_validation.pdf.gz	2.3 MB	Display
Data in XML	5hmn_validation.xml.gz	50.6 KB	Display
Data in CIF	5hmn_validation.cif.gz	68.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hm/5hmn ftp://data.pdbj.org/pub/pdb/validation_reports/hm/5hmn	HTTPS FTP

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Related structure data

Related structure data	4yfjS S: Starting model for refinement
Similar structure data	4zew-1 2wt2-1 4hmq-2 4hmq-1 5td2-1 2yqz-2 4j8m-d 2ons-d 5eow-d 5dxi-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-IDP95403

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (5) #97 - Jan 2008 Circadian Clock Proteins similarity (4) #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: AAC3-I

B: AAC3-I

C: AAC3-I

D: AAC3-I

E: AAC3-I

F: AAC3-I

hetero molecules

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

1

C: AAC3-I

E: AAC3-I

hetero molecules

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

2

D: AAC3-I

F: AAC3-I

hetero molecules

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

3

A: AAC3-I

B: AAC3-I

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.270, 62.756, 253.612
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	AAC3-I Mass: 17766.055 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: A0A059WV44
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 744 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.05 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 25% PEG3350, 0.2 M magnesium formate, 10 mM sisomycin

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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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / 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: 2.018→20 Å / Num. obs: 62091 / % possible obs: 99.7 % / Redundancy: 8.9 % / R_merge(I) obs: 0.052 / Net I/σ(I): 37.91
Reflection shell	Resolution: 2.02→2.05 Å / Redundancy: 9 % / R_merge(I) obs: 0.551 / Mean I/σ(I) obs: 4.09 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4YFJ

4yfj

Resolution: 2.018→19.868 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2209	1995	3.22 %	Random selection
R_work	0.1912	-	-	-
obs	0.1922	62004	99.57 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.018→19.868 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7220	0	253	744	8217

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	7788
X-RAY DIFFRACTION	f_angle_d	1.305	10589
X-RAY DIFFRACTION	f_dihedral_angle_d	18.037	2948
X-RAY DIFFRACTION	f_chiral_restr	0.069	1167
X-RAY DIFFRACTION	f_plane_restr	0.005	1325

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 (%)
2.0179-2.0683	0.2898	132	0.2383	4156	X-RAY DIFFRACTION	98
2.0683-2.1242	0.2646	149	0.2242	4206	X-RAY DIFFRACTION	100
2.1242-2.1866	0.2538	132	0.2169	4278	X-RAY DIFFRACTION	100
2.1866-2.2571	0.2433	152	0.2138	4244	X-RAY DIFFRACTION	100
2.2571-2.3377	0.2563	138	0.213	4242	X-RAY DIFFRACTION	100
2.3377-2.4311	0.2482	147	0.215	4277	X-RAY DIFFRACTION	100
2.4311-2.5415	0.2242	134	0.2227	4259	X-RAY DIFFRACTION	100
2.5415-2.6752	0.2843	141	0.222	4270	X-RAY DIFFRACTION	100
2.6752-2.8424	0.2505	144	0.2314	4298	X-RAY DIFFRACTION	100
2.8424-3.0611	0.2373	145	0.2231	4296	X-RAY DIFFRACTION	100
3.0611-3.3678	0.2089	138	0.1942	4299	X-RAY DIFFRACTION	100
3.3678-3.8521	0.2024	147	0.1717	4339	X-RAY DIFFRACTION	100
3.8521-4.8416	0.1823	146	0.1452	4366	X-RAY DIFFRACTION	99
4.8416-19.8689	0.2136	150	0.1855	4479	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	3.9749	-3.4268	-2.6126	3.3159	1.7973	7.7131	0.1942	0.0422	0.4397	-0.0871	-0.1731	-0.6151	-0.1693	0.0377	0.1164	0.2569	-0.0458	0.0828	0.2098	0.0035	0.3532	1.0815	20.7711	-74.1377
2	4.6644	-2.053	0.2744	8.9992	1.6248	6.2859	0.141	0.4203	0.2088	-0.4053	-0.0683	0.1603	-0.214	-0.2385	-0.0613	0.1376	-0.0238	0.0665	0.2034	0.0434	0.1956	-9.2819	17.134	-77.0776
3	3.706	0.4467	-4.0378	0.9352	-0.5184	6.3265	0.1168	-0.0606	0.0986	-0.089	0.0186	-0.1539	-0.0124	0.1795	-0.1158	0.2316	0.0264	0.0413	0.1626	0.0127	0.2658	-4.8911	12.5877	-65.2855
4	5.3219	-2.6816	-3.3946	4.0884	3.6245	3.9636	0.1911	-0.1826	0.1301	0.0342	0.1448	-0.647	-0.3137	0.4826	-0.3601	0.3084	0.0137	0.0299	0.1666	0.0104	0.3504	4.5758	8.9802	-68.1776
5	4.5805	-1.4533	-2.5525	8.4467	1.3898	4.8153	-0.1257	0.4251	-0.4727	-0.5205	-0.0764	-0.1668	0.5219	-0.1184	0.2028	0.4023	-0.0036	0.0268	0.1944	0.0168	0.3264	-3.9818	-0.6569	-65.6228
6	6.9795	-6.1218	5.4288	5.5296	-4.9235	4.396	-0.5713	0.476	0.3029	0.0638	0.0257	-0.8076	-0.176	0.2834	0.5356	0.4323	-0.0202	0.0055	0.286	-0.0299	0.4534	-20.2285	-0.1805	-67.6923
7	3.1122	4.1854	-1.4891	6.1538	-1.1005	5.9143	-0.0121	0.0561	0.5332	-0.1097	-0.1586	0.6855	-0.0472	-0.8174	0.14	0.227	0.0439	0.0577	0.2715	-0.036	0.2971	-34.7752	16.5226	-52.9924
8	2.1632	0.0898	-0.2651	2.1411	4.2522	9.2917	0.2342	-0.3077	-0.5615	0.6134	-0.0175	-0.0172	0.7737	0.0619	-0.1856	0.3246	-0.0324	-0.0125	0.2658	0.0931	0.3462	-22.1908	6.7344	-45.7854
9	5.618	-2.8696	3.7952	8.9333	-0.2561	3.0905	-0.1923	-0.1939	0.4615	0.1537	-0.061	-0.1644	-0.9287	0.2659	0.2679	0.2747	-0.0579	0.0647	0.1797	-0.0408	0.3309	-18.6807	21.0622	-51.8305
10	2.8083	0.0545	-1.3776	0.7324	0.7048	3.2969	-0.0307	0.0988	-0.4233	0.1475	-0.1102	0.095	0.3849	-0.2836	0.0383	0.2439	-0.034	0.0268	0.1401	-0.0199	0.2711	-26.2484	6.0144	-62.0635
11	5.7044	5.3666	4.696	5.1062	4.491	4.066	-0.304	-0.2965	-0.469	0.2535	0.1911	-0.2765	-0.1079	-0.3213	-0.0239	0.3751	0.0193	0.0051	0.2423	0.0116	0.4004	-7.1093	0.4491	-61.8538
12	4.2902	-5.3027	0.5447	6.745	0.0739	2.865	-0.1457	-0.2097	0.3737	0.1447	0.8747	0.2855	0.626	0.9492	-0.6081	1.5045	0.1154	0.3721	1.3793	-0.0812	1.1073	6.5213	1.4209	-47.7118
13	5.2676	-2.847	1.7633	4.7565	2.7199	7.0454	-0.071	0.7693	0.1085	-0.3728	-0.4726	0.0099	0.0687	-0.9879	0.4254	0.3546	-0.0856	0.0924	0.5358	-0.0313	0.2671	12.2937	14.2777	-42.0526
14	7.4247	0.2335	1.3383	5.6458	1.5406	4.0376	-0.4436	0.3801	-0.9787	0.2827	0.0739	0.11	0.7863	-0.2725	0.3626	0.4584	-0.1485	0.19	0.3978	-0.0415	0.2253	10.4036	7.1648	-33.6893
15	7.9073	-1.0728	-7.5774	2.8317	1.5212	8.5974	0.0363	0.318	0.1534	0.0198	-0.006	0.0976	-0.016	-0.5761	-0.0694	0.2676	-0.0462	-0.0042	0.3278	0.0008	0.1751	6.0228	19.921	-32.0016
16	7.257	-0.8785	-3.0116	3.8035	1.9329	6.4946	0.3292	0.3526	0.5149	-0.1707	0.055	-0.2209	-0.5239	-0.2121	-0.3376	0.2985	-0.0492	0.0293	0.265	0.0112	0.2269	11.9917	25.0331	-34.0123
17	7.955	0.5824	2.1676	8.9648	-3.4848	3.9523	0.5209	-1.275	-0.3137	0.9823	-0.4061	-0.906	0.0948	1.9048	-0.1	0.4605	-0.1129	-0.0147	0.9826	-0.1837	0.5286	21.1131	24.2178	-23.0198
18	6.5413	1.9205	-2.4524	2.5377	1.0061	2.7244	0.1181	-0.7285	-0.0708	0.8639	-0.0278	-0.4211	0.0625	0.3761	-0.0339	0.5682	-0.0496	-0.024	0.5262	-0.1063	0.3295	11.597	20.8015	-16.6623
19	5.3654	2.2439	-2.4452	6.7687	0.1165	3.3331	-0.2945	0.4919	-0.2036	-0.7678	0.0261	-0.3378	0.1956	-0.4669	0.3407	0.3079	0.0202	0.0768	0.4702	-0.0373	0.3312	-13.1565	-15.1928	-40.0026
20	2.3272	1.692	1.539	8.3693	0.8994	4.9867	-0.1154	-0.4154	-1.7456	0.1099	-0.1251	-1.0067	0.4836	0.7837	0.1968	0.401	0.1018	0.1875	0.8392	0.0735	0.7532	-11.3905	-24.3426	-29.3828
21	8.5004	4.5617	-5.8185	9.2803	-3.2509	4.0204	0.0478	0.4406	-0.1189	-0.0378	0.0519	0.3398	0.0864	-0.416	-0.053	0.2415	0.0027	-0.0201	0.3754	-0.0475	0.1967	-18.6114	-15.8829	-36.8123
22	3.5317	0.3459	-3.9157	2.3199	-0.7687	4.102	0.3923	-0.1717	0.3878	0.0615	-0.0681	0.3515	-0.2964	0.0926	-0.3192	0.2984	-0.0559	0.0775	0.4365	-0.017	0.3845	-25.1618	-10.7854	-27.2565
23	6.4869	1.0324	-0.9355	4.5589	0.6769	5.678	0.55	-0.1801	0.8257	0.0472	-0.2591	-0.1473	-0.5028	0.1601	-0.1668	0.2872	-0.0582	0.0784	0.3231	-0.0525	0.4094	-16.9826	-4.8553	-30.6351
24	5.0275	4.532	-4.3612	5.3373	-6.3272	7.9737	0.343	-1.4582	-0.1928	0.4706	-0.45	-1.3129	-0.4841	1.6646	0.227	0.7358	-0.1685	0.0235	1.141	-0.1373	0.5771	-15.5738	-7.501	-16.1364
25	6.7072	-0.8585	1.2319	2.5704	-1.7642	4.7486	-0.0768	0.4744	-0.4884	-0.1152	0.0415	0.8549	0.9658	-1.247	0.0052	0.7574	-0.1962	0.3391	0.8356	-0.0971	0.6858	-14.3129	9.6268	-13.3184
26	8.0092	0.6589	-1.5955	6.0636	-1.8903	3.1552	-0.0205	0.2037	0.5782	0.9277	-0.0825	1.1274	0.0554	-1.0766	0.0319	0.5222	-0.0634	0.2098	0.6817	-0.0632	0.5408	-11.2147	19.6243	-16.4881
27	3.9163	0.5466	-1.5355	1.4105	-0.9621	3.7318	-0.6134	-0.2747	-0.4557	0.9843	-0.1646	0.6303	0.6974	-0.3922	0.7744	0.6618	-0.1052	0.2269	0.4707	-0.0485	0.3698	-0.872	12.0095	-16.3868
28	5.074	-0.8035	-3.0905	0.9831	1.5655	3.4477	-0.2406	-0.5542	-0.8896	1.6118	-0.3328	0.0937	1.2799	-0.2986	0.7951	1.0542	-0.0642	0.2221	0.53	0.0291	0.3934	0.2908	8.2166	-10.1409
29	7.9801	2.4894	-2.4773	3.0656	-3.0947	3.1566	0.2533	-1.8349	-0.1567	1.4876	-0.1112	-0.5247	0.9923	-0.3337	0.0783	0.8545	-0.0021	-0.1554	0.8829	0.0129	0.4893	7.8016	18.6037	-5.048
30	5.2054	-5.3327	5.0419	5.5071	-5.224	4.9632	-0.3338	-0.6696	0.3575	0.7007	0.6369	0.02	-0.8173	-0.1625	-0.2395	0.5723	-0.0359	0.0726	0.4955	-0.0659	0.4233	10.806	26.5537	-21.2007
31	5.8847	0.7426	0.4457	5.023	-0.9632	5.8452	0.1791	-0.1093	0.7702	0.6692	0.3001	1.6675	-0.4998	-0.8345	-0.3458	0.4973	0.0243	0.2509	0.5048	0.0997	0.8166	-42.7613	-15.6749	-18.4169
32	7.2041	0.5602	-6.6704	3.2367	-1.4332	8.7693	-0.4687	-0.6377	-0.2842	0.7686	0.1797	0.2346	0.53	0.2408	0.274	0.3445	-0.0225	0.0706	0.5531	0.0414	0.3225	-30.1899	-20.0561	-18.092
33	7.2553	-6.5114	5.8022	5.8426	-5.1227	6.6199	0.3424	0.5094	-0.4165	-0.5335	-0.9834	-0.2574	0.7883	0.6009	0.6763	2.0614	0.0155	0.465	0.9784	-0.0467	0.9794	-39.7241	-15.1248	0.6553
34	8.8723	-3.0027	-4.7598	3.7843	5.3822	8.1731	0.1417	-0.3069	-0.6446	1.0228	-0.5016	-0.3966	1.0986	0.9811	0.434	0.5634	0.0582	0.0395	0.6304	0.0335	0.3609	-29.6768	-25.4978	-12.7035
35	8.6367	-0.3812	-2.5246	6.5164	-3.9131	3.2419	0.2886	-1.0185	1.051	1.2657	0.1445	-0.1559	0.4965	0.5179	-0.5365	1.2543	-0.4474	-0.1188	1.4455	-0.0496	0.7124	-24.9286	-12.313	-3.9498
36	6.1711	-4.6992	6.7039	4.0602	-4.9975	7.3445	0.2642	-1.5331	-0.5435	1.3886	-0.1964	0.7647	-0.681	-0.0262	-0.4436	0.5927	-0.2621	0.1068	1.036	0.057	0.5051	-20.5083	-3.956	-19.2001

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:19)
2	X-RAY DIFFRACTION	2	(chain A and resid 20:54)
3	X-RAY DIFFRACTION	3	(chain A and resid 55:88)
4	X-RAY DIFFRACTION	4	(chain A and resid 89:113)
5	X-RAY DIFFRACTION	5	(chain A and resid 114:141)
6	X-RAY DIFFRACTION	6	(chain A and resid 142:152)
7	X-RAY DIFFRACTION	7	(chain B and resid -1:15)
8	X-RAY DIFFRACTION	8	(chain B and resid 16:36)
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10	X-RAY DIFFRACTION	10	(chain B and resid 52:141)
11	X-RAY DIFFRACTION	11	(chain B and resid 142:152)
12	X-RAY DIFFRACTION	12	(chain B and resid 153:157)
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14	X-RAY DIFFRACTION	14	(chain C and resid 24:53)
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16	X-RAY DIFFRACTION	16	(chain C and resid 87:121)
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18	X-RAY DIFFRACTION	18	(chain C and resid 136:152)
19	X-RAY DIFFRACTION	19	(chain D and resid -1:23)
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28	X-RAY DIFFRACTION	28	(chain E and resid 93:121)
29	X-RAY DIFFRACTION	29	(chain E and resid 122:141)
30	X-RAY DIFFRACTION	30	(chain E and resid 142:152)
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35	X-RAY DIFFRACTION	35	(chain F and resid 121:141)
36	X-RAY DIFFRACTION	36	(chain F and resid 142:152)

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