PDB-7mql: AAC(3)-IIIa in complex with CoA and neomycin

ID or keywords:

Entry

Database: PDB / ID: 7mql

Title

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

Components

Aminoglycoside N(3)-acetyltransferase III

Keywords

TRANSFERASE / antibiotic resistance / aminoglycoside / acetyltransferase

Function / homology

Function and homology information

2-deoxystreptamine metabolic process / aminoglycoside 3-N-acetyltransferase / antibiotic metabolic process / 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
Revision 1.2	Oct 9, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mql.cif.gz	458.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7mql.ent.gz	378.8 KB	Display	PDB format
PDBx/mmJSON format	7mql.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mql_validation.pdf.gz	3.2 MB	Display	wwPDB validaton report
Full document	7mql_full_validation.pdf.gz	3.3 MB	Display
Data in XML	7mql_validation.xml.gz	58.3 KB	Display
Data in CIF	7mql_validation.cif.gz	84 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/7mql ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mql	HTTPS FTP

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Related structure data

Related structure data	7mqkC 7mqmC 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)	130.584, 90.882, 100.404
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-635- 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-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-RIO / RIBOSTAMYCIN / 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL / (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside Mass: 454.473 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₃₄N₄O₁₀ / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1296 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.6 Å³/Da / Density % sol: 52.76 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.2M potassium formate, 21% (w/v) PEG 3350, 2% (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 30, 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: 157232 / % possible obs: 99.81 % / Redundancy: 13.7 % / 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: 15589 / CC_1/2: 0.604

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	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→31.05 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1988	1644	1.05 %
R_work	0.1756	-	-
obs	0.1759	157232	99.83 %

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→31.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7987	0	340	1296	9623

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9149
X-RAY DIFFRACTION	f_angle_d	1.052	12594
X-RAY DIFFRACTION	f_dihedral_angle_d	19.645	1308
X-RAY DIFFRACTION	f_chiral_restr	0.061	1391
X-RAY DIFFRACTION	f_plane_restr	0.008	1591

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 (%)
1.6-1.65	0.3511	136	0.3417	12743	X-RAY DIFFRACTION	99
1.65-1.7	0.3302	136	0.3091	12809	X-RAY DIFFRACTION	100
1.7-1.76	0.2843	134	0.2682	12879	X-RAY DIFFRACTION	100
1.76-1.83	0.3147	136	0.2256	12874	X-RAY DIFFRACTION	100
1.83-1.91	0.2319	137	0.1972	12846	X-RAY DIFFRACTION	100
1.91-2.02	0.2141	137	0.1788	12948	X-RAY DIFFRACTION	100
2.02-2.14	0.195	134	0.1661	12886	X-RAY DIFFRACTION	100
2.14-2.31	0.1916	139	0.1566	12934	X-RAY DIFFRACTION	100
2.31-2.54	0.1732	136	0.1546	12994	X-RAY DIFFRACTION	100
2.54-2.91	0.199	137	0.1571	13031	X-RAY DIFFRACTION	100
2.91-3.66	0.1595	140	0.1482	13146	X-RAY DIFFRACTION	100
3.66-31.05	0.1473	142	0.1415	13498	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	0.5248	-0.0927	-0.0486	0.8794	0.4253	0.9783	-0.1092	-0.127	-0.0132	0.4429	0.0355	0.1009	0.1683	-0.0013	0.0522	0.2668	0.0339	0.0186	0.1402	-0.0163	0.1209	20.8334	37.6512	60.9857
2	0.9069	-0.3884	0.0199	1.1817	-0.3419	1.9706	0.1235	0.1976	-0.1353	-0.391	-0.1583	0.2584	-0.1835	-0.1601	0.0349	0.2633	0.0583	-0.0712	0.1494	-0.0605	0.1595	14.941	46.9381	29.9767
3	0.5937	-0.0009	-0.0368	1.4521	0.2759	0.9816	-0.0378	-0.0262	-0.0242	0.1166	0.0056	0.0128	0.0346	0.0188	0.0517	0.1051	-0.0018	0.0034	0.0989	-0.0202	0.1004	23.5169	34.6097	44.9414
4	0.3334	-0.1886	0.0891	3.1951	-0.2271	1.2998	0.0183	0.0165	0.0091	-0.0073	-0.0405	0.071	-0.1315	0.0239	0.0671	0.1532	-0.0147	0.0225	0.1279	-0.0398	0.1207	21.1767	34.2135	28.12
5	0.1763	-0.1385	-0.2956	0.1543	0.1916	0.7845	0.02	-0.0295	-0.0926	0.4335	-0.1368	0.4605	0.1424	-0.5499	0.0172	0.3799	-0.0774	0.1726	0.2224	-0.0193	0.2646	12.0575	22.4666	48.5085
6	0.5706	0.2608	0.2001	1.5446	0.7097	1.7922	-0.1214	-0.0308	-0.151	0.3717	0.0514	0.1883	0.5049	-0.0693	0.0613	0.2888	-0.022	0.0717	0.1186	-0.0076	0.1916	17.8755	18.3488	47.2272
7	0.5231	0.2237	0.1059	1.5872	0.4382	0.9844	-0.0441	0.0196	0.0291	-0.1051	-0.0166	0.1168	-0.0263	-0.0402	0.0136	0.0647	-0.0042	0.0072	0.0821	-0.0248	0.1106	18.0146	5.1397	1.954
8	0.655	0.0279	0.1749	1.5706	0.3205	0.5833	-0.0347	0.0114	0.0223	-0.0819	0.0139	0.0047	-0.0479	-0.0028	0.0451	0.0785	-0.0058	0.0085	0.0961	-0.0186	0.106	22.9553	11.8872	5.6478
9	0.3248	0.1035	0.1234	3.1348	-0.268	1.1627	0.0604	-0.0287	-0.0414	0.1365	-0.0766	0.071	0.1377	0.047	0.0563	0.1266	-0.0073	0.0008	0.135	-0.0408	0.1149	21.6943	12.5053	22.8064
10	0.3405	-0.006	0.0172	0.6442	0.6413	0.67	-0.0344	-0.0206	0.0683	-0.2646	-0.1172	0.3196	-0.0446	-0.2942	0.0636	0.2361	0.0312	-0.0979	0.2044	-0.0351	0.2799	10.5317	23.0146	2.1619
11	0.3513	-0.3961	-0.2787	1.6861	1.0026	2.1768	-0.0602	-0.0193	0.124	-0.3406	-0.0233	0.1959	-0.4313	-0.021	0.0526	0.1816	0.0125	-0.0436	0.1132	-0.0236	0.1985	16.3779	27.9385	4.1632
12	1.0699	-0.5283	0.6185	2.102	0.0587	1.8453	0.1312	0.084	0.0973	-0.5864	-0.2336	-0.1038	0.0082	0.2648	0.0792	0.2764	0.0104	0.0521	0.1766	0.0143	0.1319	52.3413	28.48	-22.435
13	0.644	-0.0351	-0.0824	1.0618	-0.342	1.1838	-0.0257	0.0724	-0.0202	-0.2528	-0.0417	-0.0995	0.1295	-0.027	0.0588	0.1316	-0.0041	0.0169	0.1142	-0.001	0.1084	47.9504	27.0276	-12.4829
14	0.2935	0.3304	0.452	0.5869	0.1045	1.7404	0.0072	-0.0748	-0.051	0.2684	-0.0431	-0.1229	-0.1815	0.0949	0.0675	0.1983	-0.0036	-0.0319	0.1323	0.0206	0.1284	50.8205	37.2426	15.9457
15	0.5533	-0.0157	-0.1772	1.1071	-0.0755	1.1067	-0.0548	0.0008	-0.0192	0.0429	0.0125	-0.0018	0.071	-0.0063	0.0574	0.0726	0.0017	0.0172	0.0966	0.0117	0.1034	44.0096	26.5791	1.9458
16	0.8329	-0.0825	-0.4373	0.9839	-0.5244	1.4151	-0.0842	0.0397	-0.1135	-0.0614	-0.0461	-0.137	0.2732	0.1349	0.0696	0.1208	0.0136	0.0366	0.1129	0.0106	0.1538	51.8342	16.9896	-1.2865
17	0.5775	-0.4887	-0.0159	2.5981	0.1132	1.3215	-0.0607	-0.0645	-0.0506	0.1288	-0.0116	-0.0049	0.0746	0.0678	0.0824	0.1544	0.009	0.0099	0.1693	0.0504	0.1264	48.2824	23.4497	17.5121
18	0.7375	-0.1006	-0.1826	0.9073	-0.2375	1.0585	-0.0414	-0.052	-0.1223	-0.0985	-0.1086	-0.2793	0.3233	0.4686	0.0777	0.1853	0.0765	0.0755	0.2244	0.0321	0.2567	60.583	13.3493	-2.7642
19	0.7723	0.3219	-0.1531	0.9058	-0.2937	1.1758	0.0433	-0.137	0.0168	0.3623	-0.1383	-0.105	-0.1209	0.0417	0.0635	0.2196	-0.033	-0.0367	0.1313	0.0152	0.1192	51.1932	18.5878	63.5257
20	0.4985	-0.3258	-0.2201	0.6524	-0.0317	1.6684	-0.05	0.1337	0.038	-0.2676	-0.022	-0.0646	0.2573	0.0019	0.0627	0.2445	-0.0353	0.0143	0.1432	0.0329	0.1244	50.2643	8.6758	32.5505
21	0.8759	0.2942	0.104	1.0159	-0.2661	0.9705	-0.0741	0.0091	0.089	0.0424	0.0283	0.0387	-0.0913	-0.0206	0.0595	0.1117	-0.0089	-0.0239	0.0993	0.0265	0.1057	45.8231	22.1671	48.4474
22	0.4328	-0.349	0.4605	1.6775	-1.3263	1.957	0.0113	0.0711	-0.0054	0.0949	-0.1242	-0.1019	-0.0696	0.3076	0.105	0.1381	-0.0513	-0.047	0.1451	0.0385	0.1611	57.3568	28.3308	46.2478
23	0.5189	0.1083	0.1493	1.8384	0.256	1.3004	-0.034	0.0595	-0.022	-0.0395	-0.0284	-0.0161	-0.0145	-0.0541	0.0639	0.1579	-0.0448	-0.018	0.1873	0.0608	0.1149	47.5036	21.0443	30.8856
24	0.473	0.1414	0.1648	0.621	-0.2287	0.5108	-0.0401	0.0294	0.0479	0.2287	-0.1162	-0.3771	-0.0544	0.4684	0.0807	0.2521	-0.0742	-0.1338	0.2445	0.0751	0.2648	64.1394	29.6281	51.2665
25	0.6036	0.4667	-0.2989	1.0971	-0.9628	2.0991	-0.0144	-0.0359	0.1195	0.2492	-0.1527	-0.2121	-0.5188	0.342	0.0365	0.2405	-0.0894	-0.0892	0.1712	0.0493	0.2082	59.883	36.1092	49.4434

Refinement TLS group

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

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Yorodumi