PDB-7mqk: AAC(3)-IIIa in complex with CoA and sisomicin

ID or keywords:

Entry

Database: PDB / ID: 7mqk

Title

AAC(3)-IIIa in complex with CoA and sisomicin

Components

Aminoglycoside N(3)-acetyltransferase III

Keywords

TRANSFERASE / antibiotic resistance / aminoglycoside / acetyltransferase

Function / homology

Function and homology information

2-deoxystreptamine metabolic process / antibiotic metabolic process / aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / acetyl-CoA catabolic process / coenzyme A binding / cellular response to antibiotic / protein homodimerization activity / identical protein binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Zielinski, M. / Berghuis, A.M.

Funding support

Canada, 1items

Citation

Journal: Plos One / Year: 2022
Title: Structural elucidation of substrate-bound aminoglycoside acetyltransferase (3)-IIIa.
Authors: Zielinski, M. / Blanchet, J. / Hailemariam, S. / Berghuis, A.M.

History

Deposition	May 5, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Aug 17, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mqk.cif.gz	447 KB	Display	PDBx/mmCIF format
PDB format	pdb7mqk.ent.gz	364.5 KB	Display	PDB format
PDBx/mmJSON format	7mqk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mqk_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	7mqk_full_validation.pdf.gz	2.5 MB	Display
Data in XML	7mqk_validation.xml.gz	55.2 KB	Display
Data in CIF	7mqk_validation.cif.gz	81 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/7mqk ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mqk	HTTPS FTP

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Related structure data

Related structure data	7mqlC 7mqmC 5ht0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#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 III

B: Aminoglycoside N(3)-acetyltransferase III

C: Aminoglycoside N(3)-acetyltransferase III

D: Aminoglycoside N(3)-acetyltransferase III

hetero molecules

125 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	130.175, 90.927, 100.048
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	D-571- HOH
2	1	D-628- HOH

#1: Protein	Aminoglycoside N(3)-acetyltransferase III / ACC(3)-III / Aminocyclitol 3-N-acetyltransferase type III / Gentamicin-(3)-N-acetyl-transferase Mass: 29947.943 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: aacC3 / Production host: Escherichia coli (E. coli) References: UniProt: P29808, aminoglycoside 3-N-acetyltransferase
#2: Chemical	ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin Mass: 447.526 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₁₉H₃₇N₅O₇ / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1332 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 52.03 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.2M potassium formate, 20% (w/v) PEG 3350, 6%(v/v) 1,3-propanediol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å
Detector	Type: Bruker PHOTON II / Detector: PIXEL / Date: Mar 10, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3418 Å / Relative weight: 1
Reflection	Resolution: 1.6→32.544 Å / Num. obs: 156548 / % possible obs: 99.85 % / Redundancy: 23.4 % / CC_1/2: 0.999 / CC star: 1 / Net I/σ(I): 20.85
Reflection shell	Resolution: 1.6→1.657 Å / Num. unique obs: 15495 / CC_1/2: 0.607 / % possible all: 99.99

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.1_3469: ???)	refinement
PROTEUM PLUS	2018.7-2	data reduction
PROTEUM PLUS	2018.7-2	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HT0

5ht0

Resolution: 1.6→32.544 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2042	1635	1.05 %
R_work	0.1795	-	-
obs	0.1797	156347	99.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→32.544 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7967	0	322	1332	9621

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8738
X-RAY DIFFRACTION	f_angle_d	1.095	12007
X-RAY DIFFRACTION	f_dihedral_angle_d	7.526	6701
X-RAY DIFFRACTION	f_chiral_restr	0.064	1347
X-RAY DIFFRACTION	f_plane_restr	0.007	1530

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 (%)
1.6-1.6471	0.3002	137	0.3146	12804	X-RAY DIFFRACTION	100
1.6471-1.7002	0.3156	133	0.2735	12730	X-RAY DIFFRACTION	100
1.7002-1.761	0.2906	138	0.2422	12807	X-RAY DIFFRACTION	100
1.761-1.8315	0.254	136	0.2018	12791	X-RAY DIFFRACTION	100
1.8315-1.9148	0.2103	132	0.178	12847	X-RAY DIFFRACTION	100
1.9148-2.0158	0.2086	135	0.171	12811	X-RAY DIFFRACTION	100
2.0158-2.1421	0.1912	134	0.1726	12802	X-RAY DIFFRACTION	100
2.1421-2.3074	0.1923	137	0.1659	12825	X-RAY DIFFRACTION	100
2.3074-2.5395	0.2221	138	0.1662	12877	X-RAY DIFFRACTION	100
2.5395-2.9068	0.2015	137	0.1657	12955	X-RAY DIFFRACTION	100
2.9068-3.6615	0.1632	136	0.1519	13040	X-RAY DIFFRACTION	100
3.6615-32.544	0.1533	142	0.1476	13423	X-RAY DIFFRACTION	100

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	0.7389	0.4398	0.6937	1.0758	0.535	2.235	-0.0131	-0.2286	0.0303	0.4014	-0.0117	0.1033	0.2273	-0.21	0.1152	0.4098	0.0933	0.0893	0.1361	-0.0342	0.0291	17.676	37.094	67.693
2	0.724	-0.0419	-0.2868	1.3189	0.5973	1.117	-0.0893	-0.114	-0.0328	0.3512	0.0528	0.0046	0.1914	0.1273	0.0337	0.145	0.0361	-0.0029	0.09	-0.0101	0.0708	21.547	37.69	57.739
3	1.2354	-0.2668	0.851	0.4082	-0.3349	3.5444	0.0673	0.1442	-0.0317	-0.3784	-0.0268	0.0793	-0.1636	-0.0712	-0.0357	0.1937	0.0236	-0.0244	0.0683	-0.0139	0.0913	14.917	46.832	30.056
4	0.571	0.0908	-0.084	1.9434	0.665	1.2019	-0.0355	-0.0037	-0.0554	0.129	0.0485	-0.0633	0.0892	0.1057	0.0009	0.0428	0.0074	-0.0003	0.0665	-0.0107	0.0569	23.551	34.492	44.588
5	0.4916	-0.0275	-0.0475	3.9586	-0.2177	1.5619	0.0347	0.0163	0.0593	-0.131	-0.0362	-0.1277	-0.1572	0.0792	0.015	0.0867	-0.0076	0.029	0.0944	-0.0308	0.0722	21.034	34.85	27.716
6	0.0505	-0.0537	-0.1937	0.2354	0.115	1.114	0.0244	-0.0808	-0.2027	0.5503	-0.0592	0.3973	0.3918	-0.3323	0.0915	0.3313	-0.0925	0.1634	0.13	0.0203	0.1961	11.794	22.457	47.852
7	0.1426	-0.032	0.1442	1.0017	0.6802	0.7468	-0.0994	-0.0378	-0.0679	0.2114	0.0197	0.235	0.3097	-0.0978	0.0837	0.2065	-0.0087	0.0496	0.1013	0.0016	0.1477	17.709	18.537	47.265
8	0.4197	0.261	-0.2095	1.7443	0.6619	0.9762	-0.1048	0.0644	0.0527	-0.5528	-0.0026	0.1051	-0.2569	0.0246	0.0571	0.1544	-0.0232	-0.0082	0.0841	-0.0057	0.0712	19.209	8.188	-9.441
9	1.29	-0.1207	-0.5197	0.963	-0.1111	2.8407	0.0207	-0.2017	0.0655	0.4695	-0.043	0.1362	0.1735	-0.0595	-0.007	0.173	-0.0361	0.0383	0.0763	-0.023	0.0822	15.916	-0.736	21.168
10	0.5779	-0.0912	0.2118	1.2138	0.2815	0.6216	-0.0243	-0.0017	0.016	-0.0645	0.015	-0.0347	-0.0506	0.0397	0.0152	0.0183	-0.0092	0.0136	0.0665	-0.0064	0.0678	22.772	11.684	5.832
11	0.4628	0.1512	0.1149	4.0866	-0.412	1.6858	0.0011	-0.0437	-0.0145	0.2421	-0.0235	-0.1621	0.1717	0.0596	0.0321	0.058	-0.0085	-0.0103	0.0814	-0.0242	0.0576	21.556	11.677	22.972
12	0.7866	-0.2187	-0.3692	0.7814	0.3034	1.6899	-0.0201	0.0239	0.1072	-0.2324	-0.0362	0.2218	-0.1799	-0.1639	0.0808	0.1338	0.0139	-0.0638	0.0785	-0.0112	0.1501	12.886	25.402	3.325
13	0.7384	-0.4413	0.6614	0.64	0.283	1.8187	0.0572	0.1396	0.0401	-0.3082	-0.0745	-0.0712	0.0406	0.2169	0.0001	0.291	0.012	0.0397	0.1066	0.0104	0.0578	52.189	28.258	-22.166
14	0.316	-0.0414	-0.0487	1.0717	-0.4683	1.3376	-0.0413	0.0063	-0.0107	-0.0103	-0.017	-0.0109	-0.0177	-0.0239	0.0208	0.0056	0.0061	0.0188	0.0559	0.0161	0.0606	48.743	32.047	0.771
15	0.8104	-0.3152	0.11	0.7805	-0.3047	1.0074	-0.0588	-0.0049	-0.0943	-0.0342	-0.0118	0.0388	0.1874	0.007	0.0664	0.0598	-0.0081	0.031	0.058	0.0097	0.0878	47.308	18.716	1.085
16	0.6602	-1.319	-0.1515	4.3544	0.4042	1.4881	-0.0966	-0.072	-0.1108	0.225	0.0509	0.2101	0.053	-0.0036	0.0569	0.0925	0.0027	0.0309	0.0884	0.0373	0.0811	48.39	23.958	17.744
17	0.2975	0.0378	-0.0832	0.3729	0.0672	0.4371	0.0074	0.0278	-0.0411	-0.1349	0.0013	-0.2169	0.0881	0.2979	0.0567	0.1363	0.0502	0.0731	0.1468	0.0306	0.1564	61.838	15.204	-3.012
18	0.8054	-0.843	0.7062	2.1824	-1.9443	3.0608	-0.0462	-0.0085	-0.0998	-0.2488	-0.0628	-0.2005	0.3559	0.2082	0.0504	0.1481	0.0546	0.0676	0.091	0.0047	0.1238	57.784	10.356	-2.639
19	0.2728	0.0148	-0.3401	0.2273	0.218	1.0386	-0.0247	-0.1445	0.0161	0.2359	-0.0154	-0.0343	0.0411	0.1423	-0.0479	0.4037	-0.0336	-0.0567	0.1087	0.0121	0.016	54.406	18.072	70.357
20	0.4976	0.343	0.3053	0.7899	-0.4464	1.3271	-0.0074	-0.0439	0.0707	0.4111	-0.173	-0.1957	-0.2609	0.0479	0.0374	0.1647	-0.0194	-0.0323	0.077	0.0281	0.0932	53.593	19.018	61.333
21	0.4599	0.0752	0.8199	1.7973	-0.9471	2.2291	-0.0239	-0.0844	0.0459	0.4422	-0.0404	0.1367	-0.2438	-0.1539	0.0473	0.143	-0.01	0.0149	0.0692	0.0023	0.0651	46.412	18.627	60.619
22	0.8498	-0.2793	-0.6838	0.2535	0.174	2.452	-0.0694	0.127	0.0027	-0.2395	-0.035	-0.0145	0.2972	-0.0844	0.0797	0.1681	-0.0337	0.0088	0.0887	0.0214	0.0721	50.327	8.488	32.73
23	0.7703	0.0128	0.1306	1.7043	-0.7172	1.6925	-0.0682	0.0666	0.0529	0.0189	0.0365	0.0911	-0.1242	-0.1051	0.0188	0.0417	-0.0099	-0.0173	0.0743	0.0169	0.0748	44.875	19.872	46.839
24	1.2971	0.1297	0.2586	1.241	-1.3379	2.1578	-0.0155	-0.0396	0.0708	0.1518	-0.0715	-0.046	-0.1907	0.1204	0.0811	0.1164	-0.0369	-0.0436	0.0654	0.0145	0.0923	53.306	28.797	49.542
25	1.1586	2.233	-0.523	4.6027	-0.7418	0.9016	-0.0933	0.0739	0.0496	-0.1179	0.0798	-0.0087	-0.0248	0.029	0.0303	0.115	-0.0288	-0.0331	0.1356	0.06	0.1026	53.082	26.388	31.481
26	2.8343	2.5015	0.6434	5.2874	1.0365	1.3364	-0.0145	-0.0168	0.0623	-0.0543	-0.1002	0.2719	0.0789	-0.3184	0.0892	0.1354	-0.0642	-0.0201	0.1851	0.0352	0.0827	43.956	17.091	30.014
27	0.3771	0.1739	0.1324	0.1835	0.1894	0.2011	-0.061	-0.0406	0.0393	0.2627	-0.0487	-0.3496	0.0083	0.3927	0.0397	0.2051	-0.0625	-0.1261	0.172	0.0587	0.163	63.945	29.648	50.587
28	0.6672	0.714	-0.7126	1.9051	-2.0369	3.0428	0.0061	-0.0252	0.0563	0.2262	-0.1151	-0.1749	-0.3754	0.2408	0.0874	0.1841	-0.0721	-0.0762	0.1105	0.0437	0.1276	59.71	35.885	49.316

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 6:20 )	A	6 - 20
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 21:64 )	A	21 - 64
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 65:100 )	A	65 - 100
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 101:181 )	A	101 - 181
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 182:210 )	A	182 - 210
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 211:241 )	A	211 - 241
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 242:265 )	A	242 - 265
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 6:64 )	B	6 - 64
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 65:100 )	B	65 - 100
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 101:181 )	B	101 - 181
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 182:210 )	B	182 - 210
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 211:266 )	B	211 - 266
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 6:20 )	C	6 - 20
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 21:125 )	C	21 - 125
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 126:181 )	C	126 - 181
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 182:210 )	C	182 - 210
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 211:241 )	C	211 - 241
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 242:265 )	C	242 - 265
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 6:20 )	D	6 - 20
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 21:43 )	D	21 - 43
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 44:64 )	D	44 - 64
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 65:100 )	D	65 - 100
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 101:150 )	D	101 - 150
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 151:181 )	D	151 - 181
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 182:198 )	D	182 - 198
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 199:210 )	D	199 - 210
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 211:241 )	D	211 - 241
28	X-RAY DIFFRACTION	28	( CHAIN D AND RESID 242:266 )	D	242 - 266

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