PDB-9mh3: Structure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) ...

ID or keywords:

Entry

Database: PDB / ID: 9mh3

Title

Structure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) in complex with acetyl coenzyme A

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 / DI(HYDROXYETHYL)ETHER / Aminoglycoside N-acetyltransferase AAC(3)-XI

Function and homology information

Biological species

Corynebacterium striatum (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.38 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	9mh3.cif.gz	207.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9mh3.ent.gz	171.8 KB	Display	PDB format
PDBx/mmJSON format	9mh3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9mh3_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9mh3_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9mh3_validation.xml.gz	22.9 KB	Display
Data in CIF	9mh3_validation.cif.gz	30.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mh/9mh3 ftp://data.pdbj.org/pub/pdb/validation_reports/mh/9mh3	HTTPS FTP

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Related structure data

Related structure data	9mgsC 9mgtC 9mguC 9mh5C 9mh6C 9mh7C 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

35.4 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)	35.422, 99.512, 39.290
Angle α, β, γ (deg.)	90.00, 106.40, 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.: 2 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₇P₃S / Feature type*: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.04 Å³/Da / Density % sol: 39.77 %
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: Apr 23, 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: 1.38→28.51 Å / Num. obs: 53467 / % possible obs: 99.89 % / Redundancy: 10.9 % / CC_1/2: 0.999 / Net I/σ(I): 15.96
Reflection shell	Resolution: 1.38→1.429 Å / Num. unique obs: 5348 / CC_1/2: 0.824

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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: 1.38→28.51 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1956	2365	2.24 %
R_work	0.1586	-	-
obs	0.1594	53467	99.58 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.38→28.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2256	0	122	351	2729

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	2700
X-RAY DIFFRACTION	f_angle_d	1.42	3706
X-RAY DIFFRACTION	f_dihedral_angle_d	26.267	420
X-RAY DIFFRACTION	f_chiral_restr	0.091	393
X-RAY DIFFRACTION	f_plane_restr	0.013	487

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 (%)
1.38-1.41	0.3495	139	0.2987	6092	X-RAY DIFFRACTION	99
1.41-1.44	0.2968	137	0.2773	5995	X-RAY DIFFRACTION	99
1.44-1.47	0.3016	139	0.2534	6067	X-RAY DIFFRACTION	99
1.47-1.51	0.2939	138	0.2337	6108	X-RAY DIFFRACTION	100
1.51-1.55	0.2471	140	0.2126	6057	X-RAY DIFFRACTION	100
1.55-1.6	0.2478	134	0.206	5970	X-RAY DIFFRACTION	99
1.6-1.65	0.2183	140	0.1906	6104	X-RAY DIFFRACTION	100
1.65-1.71	0.2625	142	0.1812	6110	X-RAY DIFFRACTION	100
1.71-1.77	0.1889	139	0.1712	6078	X-RAY DIFFRACTION	100
1.77-1.85	0.1794	139	0.1576	6092	X-RAY DIFFRACTION	100
1.85-1.95	0.2394	140	0.1521	6079	X-RAY DIFFRACTION	100
1.95-2.07	0.213	139	0.1392	6063	X-RAY DIFFRACTION	100
2.07-2.24	0.1881	141	0.1301	6075	X-RAY DIFFRACTION	100
2.24-2.46	0.1623	139	0.1424	6047	X-RAY DIFFRACTION	100
2.46-2.82	0.1579	137	0.1399	6104	X-RAY DIFFRACTION	100
2.82-3.55	0.1653	142	0.1332	6059	X-RAY DIFFRACTION	100
3.55-28.51	0.1547	140	0.1323	6030	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	2.0984	-0.5075	0.9266	1.7386	-0.9107	3.617	-0.1348	-0.0926	0.3309	-0.0452	-0.0004	0.0609	-0.5897	-0.0945	0.0689	0.1781	0.0291	-0.019	0.0934	-0.0259	0.1969	-8.0839	47.1791	-8.1064
2	2.4059	0.5858	-4.3423	0.8995	-0.3957	8.391	-0.3017	-1.1091	-0.2401	0.1925	0.5008	0.0422	0.1532	0.4811	-0.216	0.2117	0.1012	0.0109	0.5538	0.0751	0.2648	4.3076	41.1814	-0.998
3	4.7845	-0.5826	-0.1369	2.0833	-0.4897	1.0232	-0.0237	0.3105	0.4053	-0.1616	-0.0228	-0.1131	-0.0761	0.101	0.0164	0.1368	0.0051	0.0009	0.0742	0.0315	0.1649	-4.7858	41.7651	-16.3041
4	1.5559	-0.1911	-0.1122	2.6331	1.5285	2.0236	-0.0111	-0.1037	0.2354	0.0112	-0.0154	0.0949	-0.1276	-0.0582	0.039	0.0725	0.0092	0.0102	0.0536	0.0019	0.1022	-14.1525	36.6041	-7.9138
5	5.637	0.2436	4.4589	1.0026	0.583	4.9609	-0.0572	-0.0349	0.0268	-0.0153	0.0404	-0.0149	-0.1065	0.0241	0.0308	0.0725	0.005	0.018	0.0546	0.0139	0.0617	-11.4995	28.4454	-4.5554
6	3.1655	-1.0684	0.2275	7.7355	-1.458	1.2249	0.0526	-0.0855	0.0724	0.0402	-0.0475	0.1999	-0.0265	-0.1538	-0.0277	0.0622	0.0027	0.0283	0.133	0.0077	0.02	-14.6964	25.4376	3.2716
7	7.4561	2.857	-5.8893	2.0148	-2.2968	5.4207	0.1227	-0.2325	0.0704	0.0399	-0.0974	0.0067	-0.1434	0.1954	-0.0072	0.0737	0.0037	-0.0018	0.063	-0.005	0.04	1.8157	23.7486	-3.3944
8	1.4679	0.9104	-1.3506	1.8422	-1.294	4.9493	-0.0551	-0.0459	-0.0651	-0.028	0.0486	-0.021	0.3426	-0.0103	0.0479	0.1154	0.0065	0.0157	0.0586	0.0013	0.0823	-5.5424	8.5427	-19.9372
9	4.526	-4.4421	4.4452	4.9625	-4.5392	4.4079	-0.1552	-0.6236	0.0475	0.4396	0.4282	0.2042	-0.5603	-0.4596	-0.2848	0.1821	0.0244	0.049	0.3017	0.0084	0.1584	-16.1867	9.7659	-11.7151
10	8.6098	5.3882	-0.5079	7.9658	-1.1953	4.5575	-0.1361	0.0491	-0.0813	0.0346	0.1973	0.104	0.0048	-0.325	-0.0753	0.0961	0.0388	-0.0016	0.1245	0.0136	0.0394	-10.6698	16.1965	-24.8824
11	1.4956	-0.0398	0.0143	4.5763	0.5549	1.4192	0.0271	0.0705	0.0664	-0.3006	-0.011	-0.0234	-0.0067	0.0161	-0.012	0.0592	0.0132	0.0099	0.0629	0.0022	0.0465	-0.5086	22.4041	-17.7615
12	1.7858	0.2485	-0.0464	2.4393	0.1845	1.2704	0.0166	-0.1622	-0.2802	0.0121	-0.0018	0.0258	0.3096	0.0463	-0.0193	0.1273	0.0212	-0.0058	0.0727	0.032	0.0787	-0.5563	11.0159	-11.3031
13	2.4099	0.9035	-1.1766	7.2644	-0.7678	1.7658	-0.0249	0.0439	-0.0233	-0.2375	0.0351	-0.4139	0.1172	0.1844	-0.0083	0.0654	0.0268	0.0068	0.0956	-0.017	0.0735	8.6992	16.8478	-15.5287
14	2.856	-0.2336	-0.3072	1.9802	-0.3374	1.2301	-0.0596	-0.2595	-0.2739	0.0422	0.0115	0.0339	0.1952	0.1515	0.0024	0.092	0.022	0.0059	0.0945	0.0005	0.0706	1.6766	17.3541	-4.2186
15	5.7963	-1.8804	0.5322	1.1097	-0.7676	1.2979	-0.046	-0.1802	0.1428	0.0231	-0.0098	-0.0542	-0.0316	0.15	-0.0078	0.0742	-0.0046	0.0131	0.0724	0.0137	0.036	-5.7578	25.2819	0.2463

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 36 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 37 through 55 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 56 through 106 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 107 through 120 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 121 through 140 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 141 through 148 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 6 through 28 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 29 through 36 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 37 through 46 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 47 through 74 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 75 through 91 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 92 through 106 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 107 through 130 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 131 through 148 )

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