PDB-7lap: Crystal structure of aminoglycoside acetyltransferase AAC(3)-Xa

ID or keywords:

Entry

Database: PDB / ID: 7lap

Title

Crystal structure of aminoglycoside acetyltransferase AAC(3)-Xa

Components

Aminoglycoside N(3)-acetyltransferase

Keywords

TRANSFERASE / AAC(3)-Xa / RESISTANCE / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NIAID

Function / homology

aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / FORMIC ACID / D(-)-TARTARIC ACID / Aminoglycoside N(3)-acetyltransferase

Function and homology information

Biological species

Streptomyces griseus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Stogios, P.J. / Skarina, T. / Kim, Y. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: Commun Biol / Year: 2022
Title: Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.
Authors: Stogios, P.J. / Bordeleau, E. / Xu, Z. / Skarina, T. / Evdokimova, E. / Chou, S. / Diorio-Toth, L. / D'Souza, A.W. / Patel, S. / Dantas, G. / Wright, G.D. / Savchenko, A.

History

Deposition	Jan 6, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 6, 2022	Group: Database references / Category: citation / citation_author / database_2 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7lap.cif.gz	284.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7lap_validation.pdf.gz	462.6 KB	Display	wwPDB validaton report
Full document	7lap_full_validation.pdf.gz	469.3 KB	Display
Data in XML	7lap_validation.xml.gz	30.7 KB	Display
Data in CIF	7lap_validation.cif.gz	46.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/la/7lap ftp://data.pdbj.org/pub/pdb/validation_reports/la/7lap	HTTPS FTP

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Related structure data

Related structure data	5ht0C 6mmzC 6mn0C 6mn3C 6mn4C 6mn5C 7kesC 7laoC 6mn2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5wzq-2 5wzp-2 2zno-d 5uhn-d 5wzq-1 5wzp-1 5wzn-1 6ot7-d 5y2t-d 6i82-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP98166

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: Aminoglycoside N(3)-acetyltransferase

B: Aminoglycoside N(3)-acetyltransferase

hetero molecules

64.5 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)	161.489, 161.489, 138.672
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	182
Space group name H-M	P6₃22
Space group name Hall	P6c2c
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: x-y,-y,-z #7: -x,-x+y,-z #8: -x,-y,z+1/2 #9: y,x,-z #10: -y,-x,-z+1/2 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-301- CL
2	1	A-730- HOH
3	1	A-792- HOH
4	1	B-655- HOH
5	1	B-659- HOH

#1: Protein	Aminoglycoside N(3)-acetyltransferase Mass: 31817.619 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: kan, yokD_2, NCTC13033_06639 / Plasmid: pET19bTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic References: UniProt: Q54216, aminoglycoside 3-N-acetyltransferase
#2: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 4.19 Å³/Da / Density % sol: 70.66 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% (w/v) PEG3350, 0.2 M sodium tartrate, 0.25 M sodium formate Cryoprotectant: 6% (v/v) PEG200, paratone

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.04→50 Å / Num. obs: 67078 / % possible obs: 99.5 % / Redundancy: 17.2 % / B_iso Wilson estimate: 42.81 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.098 / R_pim(I) all: 0.024 / Net I/σ(I): 31.42
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 6.6 % / R_merge(I) obs: 1.074 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 3063 / CC_1/2: 0.593 / R_pim(I) all: 0.396 / % possible all: 92.9

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Processing

Software

Name	Version	Classification
PHENIX	1.15_3448	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6MN2

6mn2

Resolution: 2.04→49.39 Å / SU ML: 0.2087 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1979	3279	4.91 %	RANDOM
R_work	0.1653	63457	-	-
obs	0.1669	66736	98.86 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 54.98 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→49.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4368	0	58	658	5084

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0117	4597
X-RAY DIFFRACTION	f_angle_d	1.1177	6272
X-RAY DIFFRACTION	f_chiral_restr	0.0685	674
X-RAY DIFFRACTION	f_plane_restr	0.0078	850
X-RAY DIFFRACTION	f_dihedral_angle_d	16.5272	1673

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 (%)
2.04-2.08	0.3149	131	0.2872	2377	X-RAY DIFFRACTION	87.6
2.08-2.11	0.3271	122	0.2722	2662	X-RAY DIFFRACTION	95.9
2.11-2.14	0.2521	152	0.2574	2680	X-RAY DIFFRACTION	98.54
2.14-2.18	0.2543	127	0.2273	2763	X-RAY DIFFRACTION	99.79
2.18-2.22	0.2421	140	0.2163	2749	X-RAY DIFFRACTION	99.9
2.22-2.26	0.2848	136	0.2175	2742	X-RAY DIFFRACTION	99.9
2.26-2.31	0.2259	153	0.1968	2749	X-RAY DIFFRACTION	99.73
2.31-2.36	0.2026	160	0.1884	2731	X-RAY DIFFRACTION	99.86
2.36-2.41	0.2337	141	0.1869	2753	X-RAY DIFFRACTION	99.62
2.41-2.47	0.2331	133	0.1857	2768	X-RAY DIFFRACTION	99.55
2.47-2.54	0.2269	143	0.1842	2729	X-RAY DIFFRACTION	99.65
2.54-2.61	0.1988	151	0.1915	2745	X-RAY DIFFRACTION	99.38
2.61-2.7	0.2272	154	0.1783	2753	X-RAY DIFFRACTION	99.59
2.7-2.8	0.2226	147	0.1749	2750	X-RAY DIFFRACTION	99.31
2.8-2.91	0.2104	144	0.1837	2759	X-RAY DIFFRACTION	99.21
2.91-3.04	0.2142	135	0.1772	2772	X-RAY DIFFRACTION	99.05
3.04-3.2	0.2205	159	0.1714	2732	X-RAY DIFFRACTION	99.18
3.2-3.4	0.1882	111	0.1545	2832	X-RAY DIFFRACTION	99.49
3.4-3.66	0.1968	144	0.1468	2810	X-RAY DIFFRACTION	99.49
3.66-4.03	0.1806	140	0.1372	2819	X-RAY DIFFRACTION	99.5
4.03-4.61	0.1366	150	0.1221	2844	X-RAY DIFFRACTION	99.8
4.61-5.81	0.1669	139	0.1392	2893	X-RAY DIFFRACTION	99.9
5.81-49.39	0.2005	167	0.1807	3045	X-RAY DIFFRACTION	99.57

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	1.75917135636	2.29397398962	-0.204266552382	3.173511316	-0.399822668694	0.501660704275	0.137963495373	-0.640569791948	-2.90138594522	-0.65584550667	0.38591713092	-1.01612831024	1.04018300135	0.127017933111	-0.00416759164431	0.71670748274	0.210070377114	0.0369782739082	0.649434396442	0.180753385863	1.20047963777	46.2724275544	52.2423048724	47.04046551
2	1.31242471589	-0.47796628422	-0.273637309875	0.299595155008	-0.15728845935	0.0308243334074	-0.0735207249082	-0.274460628834	0.102192814701	-0.127617728668	-0.0135228354415	-0.329840264017	-0.210532697968	0.250618599326	-2.04649980058E-7	0.491892159394	0.0164582883991	-0.0415953130702	0.586554649672	0.0915426907266	0.496246835624	26.8367802471	61.7877770063	55.3303026164
3	2.93285315672	-0.439012140295	-0.554446144782	0.15606655877	-0.403567852559	1.74382522562	-0.0143865464888	-0.513491633753	-0.372586819361	0.00365576078729	-0.106927646359	-0.196779483468	0.23316097894	0.512997823575	-0.00114384974316	0.385253961124	0.0473911755144	-0.120024108785	0.568963874486	0.169000567336	0.4823697109	22.7482921025	52.5840084466	62.2090696633
4	1.27865380459	0.143256838652	0.683114917514	1.31744963858	0.222808953979	0.267428752353	0.100611693076	-0.134726179448	-0.47649221959	-0.328500809399	-0.0728777013655	-0.229372569033	0.422580844144	0.0307418644345	-1.3864461722E-7	0.492759484395	0.0574946683616	-0.117909903672	0.422576286085	0.0806476815826	0.537188672867	12.9656846393	48.4357939047	53.5881851301
5	3.17574585716	-0.498484346999	-1.84333776882	2.73562435183	-1.77627573349	2.66014912938	0.145396705941	0.403117988769	-0.764456244535	-0.235210736518	-0.345485727748	-1.0767157382	0.224867632333	1.07285621441	0.00591087568762	0.491702873252	0.217854927293	-0.0447791562795	0.6184161206	0.297353921662	0.84142933432	33.0543815964	44.4551577226	55.275319098
6	0.289422909807	-0.0653368996997	0.301384659306	2.82522005943	-0.571650847197	1.41018589665	0.195420449243	0.455850299052	-0.524267490151	-0.8366776094	-0.0792931250371	-0.189473582366	0.691778132415	0.370805027585	1.02307660752E-6	0.724573245219	0.0767026033728	-0.127191686519	0.561646062372	-0.0513970505328	0.691713843393	11.5507587091	45.8080807875	42.4984242036
7	2.23310529318	0.344940389851	-0.945966483462	0.303595662165	0.0477678760324	1.37331210264	-0.0617362680258	0.0611564602412	-1.12754614817	-0.277336545694	0.0769315123207	0.622748468119	0.764335233911	-0.00990182134322	-0.000894929991245	0.650988217126	0.00855866907209	-0.164688414374	0.391911636322	-0.00343849469974	0.793600740355	8.26048677953	41.1255643678	47.7866597293
8	1.85872836822	-1.14408263613	-1.2298777315	2.15820631245	-0.0709534609816	1.46786799603	0.0414551450605	0.171231608388	-0.777161374891	-0.300838737934	0.147568049093	-0.410410031963	0.604658229425	0.194256219684	0.00253575512945	0.58178510382	0.141800500515	0.0443784237656	0.599470558473	0.0310426710056	0.512047393553	44.554125469	64.2934568177	43.9693648333
9	2.59719123892	-0.311175060093	-1.16617822303	0.364931116395	0.164059057876	0.554491847648	-0.139151250503	-0.253757377776	-0.158299977934	-0.0656032086616	0.0579216982003	0.0425787364434	0.210603553754	0.225412839244	-7.20575359343E-8	0.391346735764	0.0667535473794	-0.0482720462972	0.477336609998	0.023103384437	0.34823202233	36.3600229006	75.4455045323	53.1408951983
10	0.30613661992	-0.251486974339	0.139112124694	0.245622226201	-0.0259094546176	0.111658331126	0.212329556833	-0.0693124114358	0.205716029847	-0.185806786416	0.130605027211	0.592140462451	-0.165069388375	-0.150697693303	-1.28059780827E-6	0.348666120023	0.0173389469141	-0.0627862874395	0.428451374743	0.0186297029819	0.551630484023	3.63695326405	84.2547161525	48.8724617196
11	1.63498180809	-0.748344293775	0.105592449109	0.33212795573	0.0680477578142	-0.0375727583256	0.199443973099	-0.222038035755	-0.69329269591	-0.150666740716	0.012037215606	0.192254110945	0.105482457003	0.0722037155772	8.53730734325E-7	0.438029656392	0.047297704536	-0.0581246274655	0.51719308792	0.00958162552445	0.476861479351	24.0611670874	75.098379746	55.4381319781
12	2.13612362684	0.858272786424	-0.627663136271	0.689127814962	0.263371286224	1.43757854705	0.0168802028349	-0.597350231467	0.109291466521	0.203250455893	-0.0740686322344	0.0454475895503	-0.0693530504173	0.147732387381	1.53252144538E-7	0.329369822684	0.0276235828216	-0.0184960086685	0.501671286671	-0.0640832475692	0.345315361996	28.7461508252	85.9716349901	60.2213886304
13	1.27170756002	-0.937546882774	-0.66884029211	2.69214155461	-1.09646085695	0.923081044187	0.133587976313	-0.190242544453	0.0285931485152	-0.666793049401	-0.0678918899851	0.229833663074	-0.092040046697	0.12538916325	1.01643718449E-6	0.381602578999	0.0296332135254	-0.0678693338535	0.419023200363	-0.0574460083529	0.350544034037	37.2233032139	88.2020723465	49.9823640385
14	1.20204251062	0.982917997343	0.328855387777	1.33425604236	0.456474454724	0.286646776882	0.23338782394	-0.252775718508	0.305273886409	0.0407829262921	0.00579468178545	0.354417052225	0.011855104621	-0.0102813600337	5.59572079479E-8	0.377871351176	0.0634301042768	-0.0115402400537	0.44750558352	-0.0562717997013	0.444820538363	17.4099682538	92.5528007856	54.3212492961
15	0.335121038295	-0.395775532673	0.232253241938	0.427954452482	-0.0777856393134	0.580333475346	0.072784863868	0.159890430641	-0.251408451265	-0.786104858112	0.104700793298	0.674392601744	1.28102124532	-0.273493359518	-5.45364462699E-7	0.784366168226	0.0681557179779	-0.100566971274	0.564860458581	-0.0525103001057	0.533052530992	29.0825085764	93.4288102349	35.6831135897
16	0.0917473674285	0.23562892067	-0.0938999846341	1.42092427817	0.387539841821	0.214506695824	0.121503833203	-0.116723033894	0.0446186236723	-0.521086811615	-0.0871873379612	-0.271539949443	-0.14563001931	0.263193805979	-2.11651378941E-6	0.46086746382	0.0614946205821	0.0851254113093	0.506381497663	-0.0405813431533	0.394617728825	44.8501500156	86.2076771985	40.9299830058
17	3.06705492312	0.554119414318	0.758535350554	0.900541925147	0.608535226627	1.32007964324	0.0635532891092	-0.0677724801786	0.673958044987	-0.46946528863	-0.287690786581	-0.713420890625	-0.19027691326	0.110380058378	9.76835740865E-8	0.448505598432	0.0210465479151	0.0932370157068	0.459382893005	-0.0583716355829	0.388953784746	41.1030749642	95.6729553651	42.8075645427
18	2.74699911629	-1.23779875653	1.82364982762	3.81051563437	1.10908229502	2.71271091602	0.0988216467883	0.313219806438	0.547511610508	-0.433079712787	0.070018315197	0.0620660880185	-0.273712576791	0.542603480291	0.00479221753734	0.417950082221	0.0277440116862	-0.0966118750768	0.52221670952	0.00861440186538	0.49105892866	5.56018480635	72.0362851647	46.4083723112
19	2.43956844796	-0.0725372368939	0.762728493681	0.971780576238	-0.437906784664	1.08792730124	0.065565966179	-0.0590827854618	-0.0922856923251	-0.106820321979	-0.0894271322077	-0.0438163624899	0.0912703406158	0.132916171209	-2.96774321718E-7	0.349252470989	0.0163118822491	-0.06849829238	0.380458938375	0.0311997564923	0.353147704508	14.1309460407	61.5621001885	55.3574535958

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 81 through 95 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 96 through 118 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 119 through 157 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 158 through 188 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 189 through 217 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 218 through 257 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 258 through 283 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid -1 through 26 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 27 through 80 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 81 through 95 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 96 through 119 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 120 through 157 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 158 through 188 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 189 through 217 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 218 through 235 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 236 through 257 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 258 through 283 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid -2 through 26 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 27 through 80 )

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