PDB-9mh7: Structure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) ...

ID or keywords:

Entry

Database: PDB / ID: 9mh7

Title

Structure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) in complex with coenzyme A, and one apo monomer

Components

Aminoglycoside N-acetyltransferase AAC(3)-XI

Keywords

TRANSFERASE / antibiotic resistance / aminoglycosides

Function / homology

: / acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / PHOSPHATE ION / Aminoglycoside N-acetyltransferase AAC(3)-XI

Function and homology information

Biological species

Corynebacterium striatum (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.08 Å

Authors

Zielinski, M. / Hemmings, M. / Golkar, T. / Blanchet, J. / Berghuis, A.M.

Funding support

Canada, 1items

Citation

Journal: Commun Chem / Year: 2025
Title: Enzyme-mediated aminoglycoside resistance without target mimicry.
Authors: Hemmings, M. / Zielinski, M. / Golkar, T. / Blanchet, J. / Pistofidis, A. / Munro, K. / Schmeing, T.M. / Bohle, D.S. / Berghuis, A.M.

History

Deposition	Dec 11, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 10, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9mh7.cif.gz	133.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9mh7.ent.gz	105.4 KB	Display	PDB format
PDBx/mmJSON format	9mh7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9mh7_validation.pdf.gz	695.1 KB	Display	wwPDB validaton report
Full document	9mh7_full_validation.pdf.gz	697.3 KB	Display
Data in XML	9mh7_validation.xml.gz	17 KB	Display
Data in CIF	9mh7_validation.cif.gz	22.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mh/9mh7 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/9mh7	HTTPS FTP

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Related structure data

Related structure data	9mgsC 9mgtC 9mguC 9mh3C 9mh5C 9mh6C 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 (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4)

Deposited unit

A: Aminoglycoside N-acetyltransferase AAC(3)-XI

B: Aminoglycoside N-acetyltransferase AAC(3)-XI

hetero molecules

34.4 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)	35.232, 99.900, 38.960
Angle α, β, γ (deg.)	90.00, 106.87, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Aminoglycoside N-acetyltransferase AAC(3)-XI Mass: 16713.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium striatum (bacteria) / Gene: CBE89_03745 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K2X0F2
#2: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₇P₃S / Feature type*: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.34 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, sitting drop Details: 0.1M Sodium acetate pH 4.6, 10-45% (v/v) 2-methyl-2,4-pentanediol, 0-20% (v/v) PEG 400

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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: May 3, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3418 Å / Relative weight: 1
Reflection	Resolution: 2.08→29.88 Å / Num. obs: 15419 / % possible obs: 99.41 % / Redundancy: 9.5 % / CC_1/2: 0.993 / Net I/σ(I): 15.68
Reflection shell	Resolution: 2.08→2.154 Å / Num. unique obs: 1531 / CC_1/2: 0.924

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.08→29.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2023	2972	9.98 %
R_work	0.1626	-	-
obs	0.1667	15419	97.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.08→29.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2226	0	53	136	2415

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2430
X-RAY DIFFRACTION	f_angle_d	0.568	3319
X-RAY DIFFRACTION	f_dihedral_angle_d	16.474	360
X-RAY DIFFRACTION	f_chiral_restr	0.043	366
X-RAY DIFFRACTION	f_plane_restr	0.005	442

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 (%)
2.08-2.11	0.2557	145	0.1917	1279	X-RAY DIFFRACTION	97
2.11-2.15	0.2406	138	0.1783	1245	X-RAY DIFFRACTION	96
2.15-2.19	0.2169	141	0.1745	1287	X-RAY DIFFRACTION	96
2.19-2.23	0.2315	137	0.1722	1232	X-RAY DIFFRACTION	96
2.23-2.28	0.236	133	0.1723	1240	X-RAY DIFFRACTION	95
2.28-2.33	0.2444	141	0.1863	1293	X-RAY DIFFRACTION	97
2.33-2.38	0.212	142	0.1841	1258	X-RAY DIFFRACTION	97
2.38-2.44	0.2105	143	0.1729	1288	X-RAY DIFFRACTION	99
2.44-2.51	0.2451	143	0.1933	1240	X-RAY DIFFRACTION	95
2.51-2.58	0.3041	140	0.1837	1289	X-RAY DIFFRACTION	98
2.58-2.66	0.2669	142	0.1753	1276	X-RAY DIFFRACTION	99
2.66-2.76	0.2341	142	0.1771	1284	X-RAY DIFFRACTION	97
2.76-2.87	0.2004	140	0.177	1279	X-RAY DIFFRACTION	99
2.87-3	0.2038	143	0.1646	1295	X-RAY DIFFRACTION	97
3-3.16	0.1906	145	0.1556	1291	X-RAY DIFFRACTION	99
3.16-3.36	0.1968	138	0.1502	1255	X-RAY DIFFRACTION	97
3.36-3.61	0.1845	139	0.1513	1286	X-RAY DIFFRACTION	98
3.61-3.98	0.1721	147	0.1346	1310	X-RAY DIFFRACTION	99
3.98-4.55	0.1605	145	0.1319	1279	X-RAY DIFFRACTION	99
4.55-5.73	0.1447	145	0.1473	1306	X-RAY DIFFRACTION	99
5.73-29.88	0.1962	143	0.176	1294	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	3.0647	-0.8685	-0.004	3.5089	1.6902	3.6646	-0.0093	-0.0389	-0.3802	-0.2228	0.0854	-0.156	0.0607	0.3271	-0.0533	0.1318	0.0025	0.027	0.0915	0.0144	0.1152	20.4156	31.7486	38.1311
2	2.6242	0.0918	0.0194	3.4775	0.0343	1.7709	-0.0915	0.0298	-0.0574	0.1281	0.1998	0.0845	0.1782	-0.0958	-0.084	0.0903	-0.033	0.005	0.106	-0.0039	0.0316	10.2172	38.6891	33.5176
3	4.0451	-0.1914	-1.4024	1.5995	-0.6352	2.3069	-0.0395	0.4921	-0.3898	-0.2504	-0.0612	-0.0547	0.2533	-0.3248	0.0561	0.1051	-0.0171	0.0099	0.1966	-0.0306	0.1034	10.3123	38.9051	22.4227
4	5.2164	2.5677	1.3242	1.4937	1.0565	1.0266	-0.0668	0.2349	-0.0758	-0.126	0.111	0.1022	-0.0925	-0.2277	-0.0126	0.11	0.0334	0.0225	0.1894	0.0366	0.0857	17.7566	46.6049	18.4551
5	2.3672	1.022	-0.2618	2.8812	0.6545	4.1433	-0.0291	0.2864	0.5206	-0.0836	-0.0095	0.4084	-0.6751	-0.0922	-0.0295	0.1873	-0.035	0.0016	0.1329	0.0288	0.418	18.6045	68.3549	27.4725
6	0.4571	0.7788	0.8498	3.1885	1.9204	1.689	-0.0305	0.1179	0.1081	-0.356	-0.0154	0.4605	0.5677	-1.108	0.1654	0.3617	-0.1141	0.0026	0.6318	0.0351	0.5559	6.668	62.8972	21.8299
7	6.8644	0.3459	1.0925	6.206	2.3246	7.1861	0.2553	-0.3401	0.6258	0.5506	-0.0979	0.4669	-0.2926	-0.1885	-0.1242	0.1619	-0.0239	0.0576	0.1181	-0.0455	0.3264	13.9889	63.9096	36.6637
8	1.603	0.5562	0.4175	4.6746	-0.5946	2.9128	0.0209	-0.038	0.4489	0.5888	0.0307	0.2322	-0.5375	-0.1439	-0.106	0.1286	0.0076	0.0254	0.0384	-0.0186	0.1945	22.2285	60.9327	30.7166
9	7.1345	3.643	-1.8447	8.8504	0.8899	3.46	0.039	-0.2402	-0.4306	-0.0933	0.0626	-0.7613	0.0272	0.0763	-0.0563	0.1197	-0.0112	-0.0156	0.0945	0.0246	0.0716	26.1904	42.134	36.2648
10	3.3448	-1.7708	1.182	2.4388	-1.8627	4.6842	0.1662	-0.0355	0.2463	-0.3406	0.136	0.6183	0.0579	-0.3475	-0.2578	0.0843	-0.0072	-0.0156	0.1151	0.0396	0.1911	20.6294	57.1952	25.1612
11	3.8315	-0.9255	0.8144	0.8288	-0.4491	1.4271	0.2617	0.2384	0.2168	-0.3536	-0.1504	0.0632	0.004	0.1297	0.007	0.353	-0.0947	-0.1181	0.2719	0.2942	0.3639	27.0318	69.1157	14.2938
12	1.4062	-0.6543	1.0064	4.2925	-2.4609	4.5349	-0.1082	-0.0602	0.4347	0.0678	-0.3343	-0.7011	-0.3571	0.7178	0.3119	0.1069	-0.0445	-0.0138	0.1621	0.0052	0.2077	32.1015	58.3927	28.9148
13	4.6801	0.5869	4.5898	1.6552	0.7516	8.363	0.0849	0.0675	-0.1641	-0.156	0.0667	0.1111	-0.209	-0.2452	-0.1786	0.0846	0.0193	0.0123	0.1472	0.0215	0.077	22.6566	49.9429	21.4144
14	4.0344	-1.5277	1.6873	4.7198	0.4216	5.5575	-0.367	0.9589	0.491	-0.6515	0.1572	-0.3609	-0.3761	0.2934	0.1416	0.2437	-0.0886	0.0625	0.2452	0.0436	0.175	27.0932	54.1409	12.9159
15	4.9434	0.7013	-2.1202	0.1511	-0.1766	1.4124	0.0935	0.1746	0.1565	0.0028	-0.0405	0.0012	0.0049	0.0988	-0.0032	0.0851	-0.0083	0.0121	0.1765	0.0143	0.0651	19.0277	43.8953	19.5479

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 106 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 107 through 130 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 148 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 6 through 28 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 29 through 36 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 37 through 47 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 48 through 66 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 67 through 74 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 75 through 83 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 84 through 91 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 92 through 107 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 120 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 121 through 129 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 130 through 148 )

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