PDB-7jm1: Crystal structure of aminoglycoside resistance enzyme ApmA, compl...

ID or keywords:

Entry

Database: PDB / ID: 7jm1

Title

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with acetyl-CoA

Components

Aminocyclitol acetyltransferase ApmA

Keywords

TRANSFERASE / XAT / xenobiotic acetyltransferase / left-handed beta helix / LBH / antibiotic resistance / aminoglycoside / structural genomics / CSGID / center for structural genomics of infectious diseases / NIAID / National Institute of Allergy and Infectious Diseases

Function / homology

: / Trimeric LpxA-like superfamily / transferase activity / metal ion binding / ACETYL COENZYME *A / Aminocyclitol acetyltransferase ApmA

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.31 Å

Authors

Stogios, P.J. / Evdokimova, E. / Di Leo, R. / Bordeleau, E. / Wright, G.D. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of aminoglycoside resistance enzyme ApmA, complex with acetyl-CoA
Authors: Stogios, P.J.

History

Deposition	Jul 30, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7jm1.cif.gz	402 KB	Display	PDBx/mmCIF format
PDB format	pdb7jm1.ent.gz	293 KB	Display	PDB format
PDBx/mmJSON format	7jm1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7jm1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7jm1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7jm1_validation.xml.gz	41.8 KB	Display
Data in CIF	7jm1_validation.cif.gz	58.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/7jm1 ftp://data.pdbj.org/pub/pdb/validation_reports/jm/7jm1	HTTPS FTP

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Related structure data

Related structure data	7jm0 7jm2
Similar structure data	7jm0-d 7jm2-d 3ugt-1 5f1k-d 3fvq-d 3vlc-1 6mpr-d 2awo-1 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-IDP96425

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1)

Deposited unit

A: Aminocyclitol acetyltransferase ApmA

B: Aminocyclitol acetyltransferase ApmA

C: Aminocyclitol acetyltransferase ApmA

hetero molecules

96.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	68.207, 77.233, 97.436
Angle α, β, γ (deg.)	90.000, 102.523, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Aminocyclitol acetyltransferase ApmA Mass: 31467.404 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: apmA / Plasmid: pET19bTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Gold / References: UniProt: A0A1D0AST6
#2: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₇P₃S / Feature type*: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.68 Å³/Da / Density % sol: 54.12 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M Citric Acid pH3.6, 30% PEG 200, 5mM Apramycin, 2mM AcCoA

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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: 0.97929 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2.02→40 Å / Num. obs: 42341 / % possible obs: 96.9 % / Redundancy: 2.9 % / B_iso Wilson estimate: 25.81 Å² / R_merge(I) obs: 0.046 / R_pim(I) all: 0.03 / Net I/σ(I): 17.6
Reflection shell	Resolution: 2.02→2.05 Å / R_merge(I) obs: 0.296 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 2929 / CC_1/2: 0.862 / R_pim(I) all: 0.214 / % possible all: 92.4

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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:

SAD / Resolution: 2.31→37.84 Å / SU ML: 0.1823 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.2646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1972	3597	4.73 %	RANDOM
R_work	0.1566	72518	-	-
obs	0.1586	42297	89.3 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 35.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.31→37.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6557	0	153	667	7377

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0137	6887
X-RAY DIFFRACTION	f_angle_d	1.4631	9359
X-RAY DIFFRACTION	f_chiral_restr	0.0565	994
X-RAY DIFFRACTION	f_plane_restr	0.0038	1204
X-RAY DIFFRACTION	f_dihedral_angle_d	22.3689	2544

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 (%)
2.31-2.34	0.2416	113	0.1775	2221	X-RAY DIFFRACTION	70.49
2.34-2.37	0.2387	128	0.1853	2668	X-RAY DIFFRACTION	85.74
2.37-2.41	0.2478	138	0.1914	2741	X-RAY DIFFRACTION	88.04
2.41-2.44	0.259	138	0.1883	2827	X-RAY DIFFRACTION	89.85
2.44-2.48	0.2812	140	0.1818	2752	X-RAY DIFFRACTION	89.84
2.48-2.52	0.2253	143	0.1843	2882	X-RAY DIFFRACTION	91.2
2.52-2.56	0.2501	136	0.1771	2828	X-RAY DIFFRACTION	90.15
2.56-2.61	0.2301	135	0.1699	2780	X-RAY DIFFRACTION	89.97
2.61-2.66	0.2304	143	0.1671	2830	X-RAY DIFFRACTION	89.58
2.66-2.71	0.2004	144	0.1678	2849	X-RAY DIFFRACTION	91.06
2.71-2.77	0.2044	137	0.1736	2755	X-RAY DIFFRACTION	88.82
2.77-2.84	0.2303	129	0.1733	2602	X-RAY DIFFRACTION	83.36
2.84-2.91	0.1944	136	0.1613	2780	X-RAY DIFFRACTION	89.78
2.91-2.99	0.2162	146	0.1644	2897	X-RAY DIFFRACTION	92.1
2.99-3.08	0.1756	142	0.1582	2829	X-RAY DIFFRACTION	91.16
3.08-3.17	0.2319	144	0.1563	2878	X-RAY DIFFRACTION	91.74
3.17-3.29	0.1995	138	0.1587	2860	X-RAY DIFFRACTION	91.51
3.29-3.42	0.2179	143	0.1518	2860	X-RAY DIFFRACTION	91.61
3.42-3.58	0.2139	142	0.1505	2835	X-RAY DIFFRACTION	91.29
3.58-3.76	0.1722	135	0.1405	2694	X-RAY DIFFRACTION	85.55
3.76-4	0.1575	150	0.1288	2885	X-RAY DIFFRACTION	92.5
4-4.31	0.1357	145	0.1259	2923	X-RAY DIFFRACTION	93.45
4.31-4.74	0.1457	143	0.1252	2855	X-RAY DIFFRACTION	92.27
4.74-5.42	0.1655	139	0.1382	2811	X-RAY DIFFRACTION	89.18
5.42-6.83	0.2102	134	0.1775	2865	X-RAY DIFFRACTION	91.94
6.83-37.84	0.2113	136	0.1735	2811	X-RAY DIFFRACTION	89.9

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	6.54369358688	0.674363884684	0.452995062717	3.80358175127	-0.322608059922	5.89788971099	-0.0828630058317	0.061407471004	0.0803053293847	0.122584066326	-0.0311403131807	0.104463974728	-0.000441903478867	0.113059835379	0.0773186278586	0.219596693832	0.0107457274643	-0.0113405775579	0.140109689756	0.0818785750696	0.171211130218	-18.1872803419	-4.59441604941	-34.5396972839
2	3.69177808035	-1.06436540375	-0.40903152953	0.448324203241	0.536167012452	0.390316204871	0.0652432237221	0.012202799346	0.331168755675	0.0146504838393	-0.0838474481957	-0.0171271607418	-0.113310631187	-0.0456168282779	0.00402667387427	0.173168616427	0.0187605102587	-0.00235566404732	0.151591217526	0.0115455235185	0.164662633458	-31.5187787733	-12.649825265	-9.81881765307
3	3.06893950786	0.0352138068263	0.738440247074	1.85485999483	-0.055695107519	2.11580154086	0.0916591325357	-0.282704101561	-0.47514425338	0.00343941353301	-0.132842575107	-0.318321159437	0.143147221292	0.300009518675	0.032677802673	0.143407589665	0.034342239752	-0.0173500237124	0.154744277365	0.0322531580513	0.122221923781	-11.0892935902	-26.5075917325	-7.27338347389
4	3.83526013333	0.996701519756	-1.14507743765	3.10423388146	-1.68628291929	3.23468961974	0.0785603068863	-0.00856024164655	0.337104874768	-0.114917164517	0.115214742502	0.0500059348258	-0.257913891012	-0.0556968854461	-0.148630135792	0.335695679193	0.0442325828066	-0.0192778223162	0.157425367128	-0.0435951535537	0.229768509638	-48.2848518021	-0.566585782188	-30.2932779152
5	0.82219329549	-0.707025403411	-0.358815650642	2.80800614505	2.03460622739	2.76388097009	0.0528732130996	0.176405309981	-0.241048389758	-0.194689964697	-0.178812548214	0.24811400867	0.0693332205584	-0.23163144633	0.0890423391831	0.137262120664	-0.0161166210651	-0.0119833830647	0.200361230954	-0.0627990797815	0.189992249495	-52.2072049786	-29.6778753658	-25.5721762876
6	2.39634405759	-0.835311141113	-0.892475489713	3.01058911068	0.894057351573	2.47685390593	-0.156734934274	-0.405002050023	-0.0649767457943	0.393679256179	0.0201512942562	0.452767903535	0.0871537439004	-0.153363156939	0.116384224532	0.108654801721	-0.0312845538654	0.00124170575518	0.23838970888	-0.0250021669026	0.150022917567	-56.6564941783	-18.6781048116	-2.93017497787
7	3.54222843834	-1.80328076411	0.169424805753	8.44851615534	0.443716088166	5.69280725509	-0.183646085833	0.251453860035	0.331127182333	-0.65146606368	-0.311219653692	-0.723868437092	-0.237223886471	0.395036589685	0.315954730497	0.343579258242	-0.0846101102062	-0.00715518602374	0.189983526919	-0.0194398203118	0.211229322798	-33.8440669658	-23.5201732528	-52.4828232156
8	6.74425748728	0.469765162457	3.97242180078	4.27817193225	1.56721980212	6.05756008637	-0.28801099884	1.00827476401	0.261416651524	-0.810286589556	0.00874638454946	0.421997614373	-0.945561432245	0.151633666906	0.347364102203	0.645408868381	-0.0554144049659	-0.0813951031747	0.383319374913	0.0248987739751	0.333209312761	-35.4213119175	-14.070911181	-52.91426437
9	8.28216999959	-0.777132262905	-1.91535274473	7.19608157282	-0.701742240908	5.12793365379	-0.0460092266924	0.212357363658	0.0826571464202	-0.231794685409	-0.265033967085	1.01513640627	-0.401513646896	-0.858513852683	0.230712419847	0.318596461094	0.0878765786095	-0.0801479887826	0.309426970758	-0.132745823162	0.323763502286	-44.9751359538	-19.4590772454	-48.6183175707
10	3.82044129687	1.08375538302	2.82970412598	5.73437914291	-2.76419853044	4.4935525548	-0.17406448243	0.133558872085	0.0973957915366	-0.0342546664873	0.0809249208954	-0.153706235032	-0.41449331696	0.371843440733	0.0660702473449	0.281373814407	0.00543713598095	0.00261219534723	0.288121776936	-0.0374923602339	0.143561483029	-32.1359082701	-30.7847159541	-43.1496125196
11	2.1739423431	0.377278786133	0.694596169253	2.35093416809	-1.34659411982	4.29210751613	0.0152380300431	0.231701634235	0.0966445270671	0.0326487841407	-0.0909193570888	-0.0223254775205	-0.312663004818	0.319099174424	0.0361793687451	0.183885109329	0.0166610764856	-0.00890798743619	0.193130810951	-0.0525494449551	0.14694089584	-31.8157022481	-33.4291571702	-34.2729196246
12	5.42901337046	3.34812824237	2.14570307413	2.48718818536	1.23640346787	0.837604605517	0.0533043302008	0.412043516528	-0.437827359425	-0.0382630889938	0.129403285649	-0.343029560995	0.0884406080055	0.269906861774	-0.193923589194	0.192625613394	0.0416697066138	-0.00529795265068	0.222162334305	-0.0203152690232	0.175988778346	-18.0942131794	-33.6383316713	-24.4735207728
13	4.31416992425	2.58558972458	0.421381010152	3.99573348297	3.90060167914	5.70864768297	0.094017458007	-0.307303886789	-0.343230200789	0.271551890303	-0.175830374383	0.0868416503171	0.523939810556	0.0374839537795	0.0947429133354	0.225435055934	0.0206054200876	-0.0289073350266	0.122817377039	0.0229698876901	0.210443380383	-35.9623182734	-45.1067074563	-21.3973408584
14	2.72006465437	0.0328310187611	-0.605122402816	1.51890734219	1.67836229857	9.0797509405	-0.0865191528218	0.282160069857	-0.717056977362	-0.00124745764376	0.260702395284	0.130803050612	0.801129975599	0.0655728932923	-0.0358222742519	0.288251920256	-0.0116103632788	-0.0351714551463	0.226407086236	-0.195497447675	0.464283509725	-39.341290037	-53.8786553059	-37.1183758324
15	3.06096892235	0.0398938612222	0.854863953943	4.48317959303	-3.70875700454	6.40689256308	0.00708180792899	0.43476586357	-0.978261735796	-0.951417849127	-0.171690004372	0.602435957178	0.992240032915	-0.248965941842	0.100235000271	0.456627148396	0.0112136708793	-0.0610146627146	0.337527885795	-0.224741467891	0.540182123989	-48.2284730484	-54.2260285531	-41.1532870511

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 207 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 208 through 272 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 93 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 94 through 207 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 208 through 272 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 21 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 22 through 47 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 48 through 78 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 79 through 97 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 98 through 132 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 133 through 207 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 208 through 234 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 235 through 250 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 251 through 274 )

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Yorodumi