PDB-7mqm: AAC(3)-IIIa in complex with CoA and gentamicin

ID or keywords:

Entry

Database: PDB / ID: 7mqm

Title

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

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 /

FOURIER SYNTHESIS / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mqm.cif.gz	442.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7mqm.ent.gz	368.4 KB	Display	PDB format
PDBx/mmJSON format	7mqm.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/mq/7mqm ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mqm	HTTPS FTP

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Related structure data

Related structure data	7mqkC 7mqlC 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)	130.574, 91.059, 100.524
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#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-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-51G / gentamicin C1 / (1S,2S,3R,4S,6R)-4,6-diamino-3-({(2R,3R,6S)-3-amino-6-[(1R)-1-(methylamino)ethyl]tetrahydro-2H-pyran-2-yl}oxy)-2-hydrox ycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside Mass: 477.595 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₂₁H₄₃N₅O₇ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1305 / 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: 2.61 Å³/Da / Density % sol: 52.91 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.1M MES pH 6.5, 30% w/v PEG 4000, 3% 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: Jan 27, 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→31.05 Å / Num. obs: 157949 / % possible obs: 99.38 % / Redundancy: 24 % / CC_1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 42.26
Reflection shell	Resolution: 1.6→1.657 Å / Mean I/σ(I) obs: 6.04 / Num. unique obs: 15589 / CC_1/2: 0.207 / CC star: 0.585 / % possible all: 99.7

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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:

FOURIER SYNTHESIS / Resolution: 1.6→31.048 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2161	1643	1.05 %
R_work	0.1974	-	-
obs	0.1976	156996	99.39 %

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→31.048 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7973	0	336	1305	9614

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8846
X-RAY DIFFRACTION	f_angle_d	0.741	12162
X-RAY DIFFRACTION	f_dihedral_angle_d	8.512	7152
X-RAY DIFFRACTION	f_chiral_restr	0.046	1370
X-RAY DIFFRACTION	f_plane_restr	0.005	1532

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	0.4094	136	0.3971	12839	X-RAY DIFFRACTION	100
1.6471-1.7002	0.3505	136	0.3505	12857	X-RAY DIFFRACTION	100
1.7002-1.761	0.3058	137	0.3058	12919	X-RAY DIFFRACTION	100
1.761-1.8315	0.3007	136	0.2518	12917	X-RAY DIFFRACTION	100
1.8315-1.9149	0.2853	135	0.2423	12767	X-RAY DIFFRACTION	99
1.9149-2.0158	0.2365	136	0.2037	12745	X-RAY DIFFRACTION	98
2.0158-2.1421	0.1999	136	0.1776	12816	X-RAY DIFFRACTION	99
2.1421-2.3074	0.1835	135	0.1605	12865	X-RAY DIFFRACTION	99
2.3074-2.5395	0.1711	137	0.1595	12928	X-RAY DIFFRACTION	99
2.5395-2.9067	0.1805	137	0.1615	13001	X-RAY DIFFRACTION	99
2.9067-3.6613	0.1597	139	0.1504	13162	X-RAY DIFFRACTION	100
3.6613-31.048	0.1666	143	0.1477	13537	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	0.9309	0.3544	0.3976	1.0562	-0.1448	0.266	-0.0506	-0.2986	-0.0512	0.3541	0.0293	0.0708	0.1577	-0.047	-0.0275	0.3445	0.0561	0.0311	0.1468	0.014	0.0748	18.6929	37.0294	67.9098
2	1.0343	-0.0107	-0.2208	1.227	0.6046	1.2019	-0.053	-0.1658	-0.0415	0.3693	0.0528	-0.0109	0.174	0.119	0.0037	0.1416	0.0316	-0.0066	0.0864	-0.0186	0.0682	21.8714	37.9081	58.0438
3	0.7885	0.0252	0.1504	0.3601	-0.2765	2.7016	0.1425	0.2384	-0.088	-0.4825	-0.158	0.233	-0.1367	-0.1904	-0.0082	0.2271	0.0678	-0.0589	0.1154	-0.0456	0.1409	15.0544	47.1656	30.6262
4	0.837	-0.0831	-0.2223	1.8282	0.3804	1.2917	-0.0693	-0.0322	-0.07	0.0806	0.0263	-0.0426	0.0835	0.0936	0.0393	0.0395	0.0105	-0.0081	0.0485	-0.0138	0.047	23.7113	34.7542	44.9547
5	0.4414	-0.2785	0.1105	4.4402	-0.3228	1.6774	0.0565	0.0167	-0.0284	-0.1377	-0.1301	-0.0174	-0.0773	0.0271	-0.0228	0.1399	-0.0257	0.0465	0.0854	-0.0764	0.1023	21.1424	34.2719	28.1673
6	0.6836	-0.2751	-0.8721	0.1446	0.2569	1.3744	0.0056	0.061	-0.2051	0.2265	-0.081	0.2586	0.1413	-0.432	-0.097	0.3374	-0.0763	0.1583	0.1808	0.0019	0.2936	12.0099	22.3983	48.3942
7	0.3217	0.2029	0.6136	2.0822	1.7707	2.1849	-0.0507	0.0153	-0.2125	0.2105	0.0891	0.1354	0.4069	-0.1447	-0.0408	0.2522	-0.056	0.0643	0.0913	-0.0276	0.1701	17.916	18.3101	47.2655
8	0.0674	-0.0104	-0.1121	0.0464	-0.0695	0.4866	-0.1077	0.0733	0.0345	-0.2042	0.0482	0.0388	-0.0946	-0.0042	-0.1407	0.3822	-0.0587	-0.0772	0.0649	0.066	0.0325	16.8549	9.0305	-16.6455
9	0.6277	0.1594	0.2509	1.512	0.4442	0.7958	-0.004	-0.0057	0.0261	-0.0306	-0.0047	0.0426	0.0069	0.026	-0.0101	0.0408	-0.0129	0.0125	0.0398	-0.0193	0.062	21.2672	6.9096	5.6434
10	0.1614	0.555	0.0027	1.8744	0.1914	1.7318	0.0146	-0.1172	0.0348	0.1906	-0.0581	0.0736	0.0078	-0.058	0.0407	0.0431	0.004	0.0034	0.0762	-0.0418	0.097	19.8026	14.4397	17.8594
11	0.4332	0.4518	0.69	0.4799	0.702	1.3274	-0.0074	-0.0959	0.188	-0.1871	-0.1143	0.3733	-0.1049	-0.418	0.1283	0.2286	0.0522	-0.118	0.1786	-0.0308	0.2726	10.3342	23.6428	2.5531
12	0.2883	-0.2789	-0.2289	2.5226	2.0092	2.8651	-0.0967	-0.0798	0.2234	-0.2536	0.0261	0.2371	-0.3513	-0.091	-0.0502	0.167	0.027	-0.0425	0.079	-0.0305	0.1668	16.4462	28.0291	4.1097
13	2.4201	-1.2874	0.5717	0.7278	0.0797	3.6324	0.103	0.1559	0.1081	-0.3323	-0.1029	-0.0738	-0.023	0.1585	-0.0227	0.2292	0.0128	0.0341	0.1005	-0.0027	0.054	52.1943	28.4401	-22.347
14	0.9415	-0.4916	-0.1832	0.7985	-0.4626	1.6595	0.0422	0.1144	-0.1188	-0.2636	-0.0518	0.0137	0.1321	-0.1381	-0.0107	0.0882	-0.0165	0.0231	0.0496	-0.0018	0.055	48.2819	27.2351	-12.3149
15	0.4958	0.1712	0.2691	0.9953	0.1647	1.9768	-0.0098	-0.091	0.0056	0.1868	-0.0053	-0.0828	-0.1516	0.07	0.0107	0.0815	0.0039	-0.0067	0.0431	0.0164	0.0578	49.0278	35.1691	9.0693
16	0.8563	-0.0463	-0.3327	1.0025	-0.3982	1.114	-0.0787	0.0152	-0.1298	0.0215	-0.0098	-0.0319	0.1904	-0.0064	0.0659	0.063	-0.0012	0.0376	0.0416	0.0083	0.078	47.4493	18.7755	1.2305
17	1.246	-2.7801	0.0723	6.4949	-0.0806	1.299	-0.1148	-0.0287	-0.1377	0.2211	-0.0245	0.0762	0.1124	0.1504	0.1323	0.0924	0.0157	0.0232	0.1402	0.0508	0.1201	51.3769	20.4779	16.8082
18	1.5695	-1.7505	-0.5559	4.8159	1.6867	2.5221	0.085	-0.0404	-0.1223	-0.0561	-0.2411	0.2197	-0.1004	-0.2867	0.0658	0.151	0.0312	0.0138	0.1452	0.0576	0.0619	44.1807	28.6535	18.8895
19	0.5875	-0.5317	-0.5421	1.0832	-0.1428	1.3729	-0.1031	-0.1864	-0.1465	0.142	0.0504	-0.1167	0.111	0.4433	-0.1403	0.1361	0.0868	0.1218	0.2562	0.0276	0.2999	62.1759	15.281	-2.5943
20	0.3228	-0.4033	0.1611	1.8567	-1.1288	2.1312	-0.0781	-0.089	-0.194	0.0084	-0.0974	-0.2546	0.3566	0.3832	0.0636	0.161	0.0673	0.0542	0.1226	0.0388	0.2062	57.8918	10.4317	-2.6824
21	0.8801	0.2705	0.1752	0.4684	0.8962	2.0501	0.0184	-0.1717	-0.005	0.1907	-0.0234	-0.0281	0.0877	0.0553	-0.1339	0.3	-0.0574	-0.0635	0.127	-0.0227	0.0472	54.5413	18.1792	70.6437
22	1.3481	-0.0752	0.423	1.0102	-0.6837	1.7293	0.0279	-0.0835	0.0428	0.2554	-0.1497	-0.0373	-0.0725	-0.0663	-0.0381	0.1078	-0.0232	-0.0261	0.0488	0.0258	0.0565	50.1981	18.8478	61.0204
23	1.165	-0.5406	-0.3619	0.8384	0.2255	2.7293	-0.0292	0.1823	0.0129	-0.3017	-0.0061	-0.1039	0.2849	0.022	0.0389	0.1887	-0.0389	0.0035	0.102	0.0258	0.0921	50.2591	8.6374	32.5713
24	0.6548	-0.1525	-0.1201	1.1832	-0.5246	1.5915	-0.1056	0.115	0.1031	-0.0141	0.0311	0.0776	-0.0735	-0.1128	0.0076	0.0495	-0.0233	-0.031	0.0633	0.0326	0.0595	45.0355	19.5323	47.4245
25	1.4886	-0.0219	0.538	2.1856	-1.6702	2.1628	-0.1172	0.0464	0.1283	0.0789	-0.0168	-0.0581	-0.1465	0.083	0.1025	0.0899	-0.0297	-0.0512	0.0519	0.0167	0.0983	53.5088	29.0209	49.7454
26	0.9426	1.7196	-0.2664	3.9074	-0.1705	0.674	-0.0683	0.0815	0.0591	-0.1347	0.0027	-0.0367	-0.0941	0.07	0.0384	0.1333	-0.0443	-0.0414	0.1759	0.073	0.1354	52.4205	25.8154	31.9117
27	0.7312	1.1298	-0.2688	4.4161	0.2834	1.5914	-0.0092	0.0796	0.0101	0.0228	-0.0568	0.2999	0.1403	-0.2622	-0.2709	0.1883	-0.1159	-0.0321	0.2253	0.0909	0.0732	43.6669	17.1642	30.1258
28	0.0721	-0.0597	0.1643	0.3339	0.0575	0.9377	0.0238	0.044	0.0899	0.0835	-0.0427	-0.2804	-0.1525	0.4307	0.0378	0.1863	-0.1114	-0.1184	0.1693	0.0762	0.2298	62.0855	32.7557	50.1515

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 64 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 100 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 101 through 181 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 182 through 210 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 211 through 241 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 242 through 266 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 7 through 20 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 21 through 165 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 166 through 210 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 211 through 241 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 242 through 266 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 6 through 20 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 21 through 64 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 65 through 125 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 126 through 181 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 182 through 198 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 199 through 210 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 211 through 241 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 242 through 265 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 6 through 20 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 21 through 64 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 65 through 100 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 101 through 150 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 151 through 181 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 182 through 198 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 199 through 210 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 211 through 266 )

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