PDB-6mn1: Crystal structure of meta-AAC0038, an environmental aminoglycosid...

ID or keywords:

Entry

Database: PDB / ID: 6mn1

Title

Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, mutant H168A in abortive complex with gentamicin-CoA

Components

Aminoglycoside N(3)-acetyltransferase

Keywords

TRANSFERASE/ANTIBIOTIC / ANTIBIOTIC_NAT FAMILY /

ACETYLTRANSFERASE /

AMINOGLYCOSIDE /

ANTIBIOTIC RESISTANCE /

METAGENOME / SOIL /

COENZYME A / CSGID /

TRANSFERASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES /

National Institute of Allergy and Infectious Diseases / NIAID / TRANSFERASE-ANTIBIOTIC complex

Function / homology

Function and homology information

aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / response to antibiotic
Similarity search - Function

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Stogios, P.J. / Skarina, T. / Michalska, K. / Xu, Z. / Yim, V. / Savchenko, A. / Joachimiak, A. / Satchell, K.J. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201200026C	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	HHSN272201700060C	United States

Citation

Journal: To Be Published
Title: Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, mutant H168A in abortive complex with gentamicin-CoA
Authors: Stogios, P.J.

History

Deposition	Oct 1, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mn1.cif.gz	239 KB	Display	PDBx/mmCIF format
PDB format	pdb6mn1.ent.gz	191.3 KB	Display	PDB format
PDBx/mmJSON format	6mn1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mn/6mn1 ftp://data.pdbj.org/pub/pdb/validation_reports/mn/6mn1	HTTPS FTP

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Related structure data

Related structure data	5ht0S S: Starting model for refinement
Similar structure data	7kes-d 5ht0-1 5ht0-2 6mmz-1 6mn0-2 6mn2-d 6mmz-3 6mn0-3 5ht0-3 5m63-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP95753

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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 N(3)-acetyltransferase

B: Aminoglycoside N(3)-acetyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	127.337, 127.337, 95.271
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-659- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Aminoglycoside N(3)-acetyltransferase Mass: 28654.350 Da / Num. of mol.: 2 / Mutation: H168A 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)-Magic References: UniProt: A0A059X981, aminoglycoside 3-N-acetyltransferase

#1: Protein

Aminoglycoside N(3)-acetyltransferase

Mass: 28654.350 Da / Num. of mol.: 2 / Mutation: H168A
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)-Magic
References: UniProt: A0A059X981, aminoglycoside 3-N-acetyltransferase

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Non-polymers , 7 types, 604 molecules

#2: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-LLL / (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL / GENTAMICIN C1A Mass: 449.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₃₉N₅O₇
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₈H₅₈O₁₅
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 585 / 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: 3.9 Å³/Da / Density % sol: 68.43 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.6, 35% PEG5K, 10 mM gentamicin

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 24, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97919 Å / Relative weight: 1
Reflection	Resolution: 2.25→30 Å / Num. obs: 42543 / % possible obs: 100 % / Redundancy: 17.4 % / R_merge(I) obs: 0.143 / Net I/σ(I): 20.48
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 12.8 % / R_merge(I) obs: 2.007 / Mean I/σ(I) obs: 1.48 / CC_1/2: 0.641 / R_pim(I) all: 0.577

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Processing

Software

Name	Version	Classification
PHENIX	(DEV_3092: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HT0

5ht0

Resolution: 2.25→29.12 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.55

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21	3857	4.71 %	RANDOM
R_work	0.177	-	-	-
obs	0.178	81856	99.9 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.25→29.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3987	0	239	585	4811

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4317
X-RAY DIFFRACTION	f_angle_d	0.811	5869
X-RAY DIFFRACTION	f_dihedral_angle_d	22.888	1614
X-RAY DIFFRACTION	f_chiral_restr	0.048	633
X-RAY DIFFRACTION	f_plane_restr	0.004	739

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 (%)
2.2504-2.2779	0.3243	133	0.302	2787	X-RAY DIFFRACTION	99
2.2779-2.3067	0.306	130	0.3014	2781	X-RAY DIFFRACTION	100
2.3067-2.337	0.334	140	0.2958	2794	X-RAY DIFFRACTION	100
2.337-2.369	0.3172	136	0.2814	2777	X-RAY DIFFRACTION	100
2.369-2.4029	0.3014	140	0.2797	2809	X-RAY DIFFRACTION	100
2.4029-2.4387	0.3002	138	0.2763	2761	X-RAY DIFFRACTION	100
2.4387-2.4768	0.2977	144	0.2627	2775	X-RAY DIFFRACTION	100
2.4768-2.5174	0.2641	134	0.245	2791	X-RAY DIFFRACTION	100
2.5174-2.5608	0.2832	140	0.2438	2798	X-RAY DIFFRACTION	100
2.5608-2.6073	0.2513	136	0.2497	2795	X-RAY DIFFRACTION	100
2.6073-2.6574	0.3368	132	0.2469	2767	X-RAY DIFFRACTION	100
2.6574-2.7116	0.2653	138	0.2312	2780	X-RAY DIFFRACTION	100
2.7116-2.7706	0.237	138	0.2318	2792	X-RAY DIFFRACTION	100
2.7706-2.8349	0.319	142	0.2335	2774	X-RAY DIFFRACTION	100
2.8349-2.9058	0.2255	142	0.2283	2801	X-RAY DIFFRACTION	100
2.9058-2.9843	0.2542	135	0.2243	2765	X-RAY DIFFRACTION	100
2.9843-3.072	0.2548	146	0.2091	2796	X-RAY DIFFRACTION	100
3.072-3.171	0.212	140	0.2012	2771	X-RAY DIFFRACTION	100
3.171-3.2842	0.2285	135	0.1714	2805	X-RAY DIFFRACTION	100
3.2842-3.4155	0.167	136	0.1577	2771	X-RAY DIFFRACTION	100
3.4155-3.5707	0.1887	142	0.1558	2773	X-RAY DIFFRACTION	100
3.5707-3.7586	0.1829	144	0.1461	2819	X-RAY DIFFRACTION	100
3.7586-3.9935	0.1618	130	0.129	2783	X-RAY DIFFRACTION	100
3.9935-4.301	0.1643	134	0.1207	2801	X-RAY DIFFRACTION	100
4.301-4.7322	0.1615	134	0.1179	2786	X-RAY DIFFRACTION	100
4.7322-5.4131	0.1323	142	0.1227	2772	X-RAY DIFFRACTION	100
5.4131-6.8055	0.2387	130	0.1478	2801	X-RAY DIFFRACTION	100
6.8055-29.1239	0.1628	146	0.1522	2774	X-RAY DIFFRACTION	99

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	2.0412	-0.7185	0.4295	2.6471	0.5252	3.674	0.0039	-0.0579	-0.0605	-0.1735	0.0092	-0.2619	-0.0253	0.3516	-0.0232	0.2066	-0.0693	0.0126	0.3447	-0.0146	0.3737	212.522	277.096	-1.6916
2	3.1278	0.1748	-0.242	0.6056	-0.3504	2.0478	0.0503	0.0118	0.1599	-0.0178	0.1324	0.2243	-0.324	-0.6128	-0.1442	0.207	0.0287	0.0222	0.4032	0.0781	0.3518	189.2127	279.8174	-0.388
3	3.0366	-1.0214	-1.4773	0.8347	0.3171	2.2621	-0.1509	-0.4209	-0.3619	0.1953	0.1083	0.2484	0.2898	-0.3884	0.0404	0.2062	-0.0526	-0.0085	0.4647	0.0999	0.3721	192.5962	269.788	9.0705
4	2.4639	0.1138	-0.0419	0.9746	0.2746	1.8646	-0.0378	-0.4221	-0.0442	0.1255	0.1414	-0.0629	0.0241	-0.2095	-0.0994	0.2174	-0.0588	0.0098	0.4143	0.0106	0.2963	201.1383	277.6172	13.4481
5	2.99	0.5544	2.1568	0.9641	0.1611	4.9476	0.0927	-0.8371	0.6176	0.242	-0.2598	0.2829	-0.6655	-0.8294	0.042	0.3914	0.0019	0.1029	0.7793	-0.0112	0.4253	183.5995	282.4153	17.1798
6	1.5531	-0.3644	-0.5639	1.751	-0.6982	0.5774	-0.0445	0.0575	-0.0809	0.0705	0.0962	0.3383	-0.2256	-0.3163	-0.0068	0.2405	0.0002	0.0759	0.6949	0.1053	0.4452	177.4613	276.4122	7.3822
7	4.5806	2.145	0.2845	3.3178	0.5558	5.0614	0.0079	0.2037	1.2837	-0.3269	0.2348	0.6165	-1.0923	-0.7737	-0.317	0.536	0.0886	0.0805	0.585	-0.0983	0.6023	193.1291	291.2418	18.4073
8	1.6541	0.2602	0.0963	0.4366	0.4335	1.8843	0.0618	-0.1808	-0.018	0.1415	-0.0461	-0.193	-0.2989	0.4536	-0.053	0.3279	-0.1278	-0.0218	0.4521	-0.0118	0.3901	211.259	284.2887	15.1756
9	3.4327	0.5595	-0.4187	2.3244	-0.7843	3.2361	0.113	-0.7971	0.1169	0.5254	0.0503	0.0192	-0.281	-0.1065	-0.1858	0.328	-0.0838	-0.0236	0.5551	-0.0318	0.297	203.6257	281.7404	22.9218
10	3.3153	0.3071	-0.7887	0.3754	-0.9923	4.0221	0.3258	0.8985	0.4918	-0.3258	-0.0124	0.357	-0.4156	-1.2828	-0.3132	0.3816	0.1258	-0.0037	0.9246	0.252	0.5781	177.8522	285.9312	-20.4564
11	2.6997	-0.8151	-0.3293	1.0712	-0.5358	3.1205	0.0712	0.3499	0.0935	0.1677	0.1605	-0.0126	-0.2506	-0.8376	-0.2257	0.3446	0.1123	0.0598	0.7519	0.252	0.4622	182.5619	285.6334	-14.6767
12	2.8237	-1.0235	-0.96	0.7768	-0.2174	2.6868	-0.0273	0.5833	0.0596	-0.1833	0.1001	-0.0566	0.0184	-0.4153	-0.0633	0.2668	-0.0908	0.0369	0.4212	0.0404	0.3094	200.2359	276.4664	-22.3633
13	2.5818	-0.8308	-0.6533	1.0897	0.6252	1.3176	0.1531	0.9869	0.3082	-0.3734	-0.0012	-0.1371	-0.3104	-0.598	-0.1425	0.4432	-0.0463	0.0851	0.7344	0.1419	0.3796	201.0572	279.4512	-32.6547
14	0.3085	-0.5467	-0.4254	1.0014	0.4089	1.1031	0.3726	0.7941	0.5747	-0.4968	-0.1065	-0.1234	-0.6806	-0.6666	-0.1767	0.7563	0.2297	0.1849	1.0653	0.4116	0.6515	191.2729	293.429	-34.5586
15	1.5251	-0.6254	-0.1041	0.672	0.7512	1.5125	0.5607	1.1042	0.8333	-0.6772	-0.1873	0.0882	-0.8189	-0.5056	0.107	0.7644	0.2531	0.0738	1.5142	0.5208	0.4035	190.4643	289.1263	-41.4863

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 3 THROUGH 53 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 54 THROUGH 117 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 118 THROUGH 142 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 143 THROUGH 173 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 174 THROUGH 189 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 190 THROUGH 202 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 203 THROUGH 214 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 215 THROUGH 236 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 237 THROUGH 262 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 3 THROUGH 30 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 31 THROUGH 53 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 54 THROUGH 142 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 143 THROUGH 202 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 203 THROUGH 236 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 237 THROUGH 261 )

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