PDB-7jm0: Crystal structure of aminoglycoside resistance enzyme ApmA, apoenzyme

ID or keywords:

Entry

Database: PDB / ID: 7jm0

Title

Crystal structure of aminoglycoside resistance enzyme ApmA, apoenzyme

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 / Aminocyclitol acetyltransferase ApmA

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.08 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, apoenzyme
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 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7jm0.cif.gz	392.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7jm0.ent.gz	284.4 KB	Display	PDB format
PDBx/mmJSON format	7jm0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7jm0_validation.pdf.gz	441.2 KB	Display	wwPDB validaton report
Full document	7jm0_full_validation.pdf.gz	443.8 KB	Display
Data in XML	7jm0_validation.xml.gz	35.7 KB	Display
Data in CIF	7jm0_validation.cif.gz	52.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/7jm0 ftp://data.pdbj.org/pub/pdb/validation_reports/jm/7jm0	HTTPS FTP

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Related structure data

Related structure data	7jm1S 7jm2 S: Starting model for refinement
Similar structure data	7jm1-d 7jm2-d 5f1k-d 2awo-1 6mpr-d 1lk5-d 5v13-d 20051 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

93.7 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)	68.544, 76.916, 96.572
Angle α, β, γ (deg.)	90.000, 102.121, 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: 31196.191 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.66 Å³/Da / Density % sol: 53.81 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 5% 2-Propanol, 0.1 M Citric acid pH 3.5, 6% PEG 20K cryoprotectant 25% ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.08→25 Å / Num. obs: 58261 / % possible obs: 98.7 % / Redundancy: 3.2 % / B_iso Wilson estimate: 33.18 Å² / R_merge(I) obs: 0.109 / R_pim(I) all: 0.075 / Net I/σ(I): 19.39
Reflection shell	Resolution: 2.08→2.12 Å / R_merge(I) obs: 0.451 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 2886 / CC_1/2: 0.771 / R_pim(I) all: 0.297

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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: 7JM1

7jm1

Resolution: 2.08→25 Å / SU ML: 0.2235 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.6242
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2223	2000	3.43 %	RANDOM
R_work	0.1883	56230	-	-
obs	0.1894	58230	98.32 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 36.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.08→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6573	0	5	581	7159

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	6769
X-RAY DIFFRACTION	f_angle_d	0.526	9185
X-RAY DIFFRACTION	f_chiral_restr	0.0459	984
X-RAY DIFFRACTION	f_plane_restr	0.0032	1202
X-RAY DIFFRACTION	f_dihedral_angle_d	19.7097	2474

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 (%)
2.08-2.13	0.2712	138	0.2202	3867	X-RAY DIFFRACTION	95.36
2.13-2.19	0.285	145	0.2112	4079	X-RAY DIFFRACTION	99.98
2.19-2.25	0.2765	144	0.2063	4051	X-RAY DIFFRACTION	99.9
2.25-2.32	0.2529	143	0.1975	4031	X-RAY DIFFRACTION	99.95
2.32-2.41	0.2615	145	0.2032	4074	X-RAY DIFFRACTION	99.86
2.41-2.5	0.2431	144	0.1983	4055	X-RAY DIFFRACTION	99.79
2.5-2.62	0.2374	144	0.1948	4043	X-RAY DIFFRACTION	99.43
2.62-2.76	0.2474	145	0.1957	4079	X-RAY DIFFRACTION	99.27
2.76-2.93	0.2181	143	0.1937	4012	X-RAY DIFFRACTION	98.81
2.93-3.15	0.2143	142	0.1932	3994	X-RAY DIFFRACTION	98.15
3.15-3.47	0.2076	141	0.1858	3974	X-RAY DIFFRACTION	97.07
3.47-3.97	0.1935	140	0.1703	3930	X-RAY DIFFRACTION	95.7
3.97-5	0.192	140	0.1647	3932	X-RAY DIFFRACTION	95.45
5-25	0.2343	146	0.2001	4109	X-RAY DIFFRACTION	97.88

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	1.37000261133	1.11169444256	-0.593228934248	2.6567470851	1.06412443774	1.66918915676	-0.0278448515046	0.118645709006	0.208141450503	-0.568862510839	-0.0454401519577	-0.165663953069	-0.39580014031	0.0123269355575	-0.000790529906624	0.410766863335	0.0232832059128	-0.0344621911539	0.303693258598	-0.0143865436563	0.256756710834	-11.5888326225	-18.3479020189	-5.11844921448
2	0.465066399983	0.118547173722	-0.504647802137	0.755295363189	-0.213416407825	0.613302274994	0.0233467487765	0.13950883595	0.00508437185165	0.13237412777	-0.512907200611	0.840394786817	0.0310652140249	-0.660984404319	-0.00721895672148	0.332014039373	0.0360722596716	-0.0863185435329	0.475468880097	-0.136574696332	0.478690987624	-22.9396869259	-19.9069423379	-0.796633254378
3	0.0849192125527	0.028845069881	0.0669310219562	0.326546292883	-0.386440410953	0.518166247994	0.0104477684486	-0.0933382037698	0.195639037937	-0.0382428036965	0.0627522463788	-0.170991006012	-0.399608215655	0.295603543806	2.4577939433E-8	0.289750515219	0.0141325220459	-0.00453652340082	0.367454539316	-0.000422066617086	0.266995560801	-8.77120728426	-30.4797332817	4.49199422405
4	1.35473980949	-0.257085421501	-0.594644034326	0.982915412204	-0.895486597163	1.58994264987	-0.0146853077022	0.0762275595338	0.164661526962	0.230324727998	-0.00958501592931	-0.127376745815	-0.290332725418	0.192047489129	-5.17299322075E-7	0.257510036221	0.00117367612743	-0.0206197354015	0.254208697954	-0.0284423884131	0.230236526897	-8.35686024249	-33.1565075614	13.3587370776
5	1.73149766027	1.39124996354	0.902931913768	0.722513443169	0.840540182063	0.380793211723	0.100933505609	-0.0547734810588	-0.360482613466	0.0710722861708	-0.0260603073843	-0.189319397457	0.0236331627139	0.048760341029	-0.000115618375567	0.349161602623	0.0142250536692	-0.0339977660432	0.310307038347	0.000401823997777	0.340701753947	0.584548268713	-36.3561499055	23.9213651175
6	0.970514650514	-0.119136031214	-0.736191121569	1.25555308918	0.175016129068	0.583719178773	-0.0465104537408	0.258796518602	-0.622975480554	-0.166880209856	-0.0832263484902	0.315523826691	0.276761636877	-0.15711882838	-3.3687429134E-5	0.402501393788	-0.0152344655178	-0.0452148313356	0.328185879849	-0.112605917567	0.521328444549	-20.8557011553	-53.846992558	8.22594576424
7	0.739142865316	-0.307802482504	0.493166579234	0.823183671648	-0.402500147953	0.396782666179	-0.0631419339541	-0.103896676576	-0.00912654777269	0.189162366107	0.116944878689	-0.0142996839786	-0.614005921615	-0.105245204885	-1.31611579236E-7	0.367478620149	0.00604521186751	-0.0372860667354	0.320893193016	0.0364533246101	0.282897236457	6.65693212068	-1.3866071244	18.5604581773
8	0.603022989105	-0.366055491538	0.290778267294	0.240194546886	-0.169865220415	0.106709136414	-0.0629742682657	-0.158797887285	0.984960152216	0.18329428327	0.0920767392814	-0.351198345649	-0.612210712321	0.0508675085545	1.5020106056E-7	0.389454785328	0.00162770520843	-0.0795107536555	0.386636024556	-0.0644104098606	0.545642545561	-2.27840301685	1.90292244515	13.1112564829
9	0.629821975316	0.079982672494	0.359756512457	0.896203669506	-0.338048808321	0.71427390785	0.0146776610844	0.289554370675	-0.478842080099	-0.00495276438821	-0.0369850484842	-0.0936338737661	0.396247665987	0.25873509694	-1.9594948376E-5	0.308678928534	0.049090909376	-0.0154922875504	0.318360912548	0.00748129000871	0.297442102766	7.6492901914	-9.68411010735	9.48140277168
10	0.635414489963	0.0639727028202	-0.224683804059	0.334625266855	-0.50421013163	0.562849499597	-0.0419019281129	0.203876940956	0.210744219911	0.081933071742	0.155871933521	0.173191072566	-0.214698414197	-0.270425092656	-1.10003271539E-7	0.317709142649	0.0352325300849	-0.0308341365783	0.343573002984	0.0458090837085	0.267684255361	1.82677551165	-10.2397886112	28.689546075
11	0.36966294566	-0.264851451641	-0.497399144931	0.884529752939	-0.194349688987	0.855528211029	0.0564170149519	0.416262511169	0.0166353668352	0.0719737098583	-0.103183062131	0.583539641617	0.0139383319315	-0.723185679837	-0.00422471231259	0.307566829918	-0.00420761803683	-0.0285935904743	0.420387133067	-0.00622023872558	0.319561889154	-1.78576374526	-16.0049635977	34.2637807871
12	2.32204444229	-0.732113914234	-0.273868565711	-0.0766115794162	-0.0554166965716	-0.517855389209	-0.173019900322	-0.171031851805	0.020507816187	0.0904550579527	0.0500357237664	-0.0039166767137	-0.0379263254748	0.0959482358572	-0.000951904772321	0.308671390841	0.03604675652	0.0082553723989	0.356657301615	-0.0105049157624	0.307063412512	-16.6183338316	-10.7805538289	42.6378624631
13	0.435559493456	-0.527128577834	0.0610369271783	0.630081091659	-0.127899518993	1.13127633769	0.0028149289517	-0.0341497744496	-0.510901918179	0.13877937159	-0.026511095156	0.472659049542	0.300488587508	-0.424578761681	-0.0046284073955	0.291141688359	-0.0375211534832	0.00645882352043	0.356551797857	0.045347123493	0.346930933267	-0.927935190671	-26.6912833548	41.8072616192
14	0.628613565009	0.368772453204	0.299286390779	0.391646407628	0.433343456549	0.460442674507	-0.105500868117	-0.389953325021	-0.259279264056	0.678529063079	-0.0924381127189	-0.4266613012	-0.133612501485	0.190681849777	-0.000128367507602	0.303568805079	0.0186742654488	0.00860141110015	0.343050628459	0.0394389258152	0.277279576336	16.8308148593	-21.9688986223	42.8908040183
15	0.78169354501	0.154566429441	0.403978883798	0.553073380848	0.532286489118	0.639434165055	-0.0905463434983	-0.0562447758105	-0.286178356067	0.152134989217	0.0315777295897	-0.72125075452	0.126317335963	0.312638111424	-9.70304192819E-8	0.291474619228	-0.0173484813833	0.0167185058369	0.310031981816	0.00527103644051	0.367576842277	23.4763258335	-25.4088619214	35.7342823969
16	2.33840763322	0.559969150633	-1.1072135504	1.78199260308	-1.09994138136	2.59852981244	0.00970386947975	0.0181151372296	0.173457150362	-0.0120221586774	0.00972590061526	0.0759849740105	0.0025896615125	-0.0924338125057	-9.95372346031E-8	0.334134746683	0.0170836967006	0.0124839084548	0.270189102767	-0.0504070114493	0.345546195331	-25.1333998647	-0.970553603631	17.2273358892
17	0.0128908513034	-1.4314740948	-0.492359059858	1.60559935804	1.91738582373	1.57167239195	0.0466887278995	0.0549321192587	-0.0802454589313	-0.00202318918796	-0.0638530938352	0.196364533632	-0.0771126126291	-0.0852680335568	-0.00104398876283	0.316083290296	-0.0533860718286	0.0804197128926	0.294907908739	-0.0632848962251	0.381945789119	-28.6205358306	-29.826105163	21.9063808512
18	1.64328363804	1.31228565399	0.305917793418	1.90316478717	-0.442751771729	2.73934814653	-0.0256153678761	-0.389801846053	-0.0744737277072	0.310266738023	-0.00431901524389	-0.0638225805175	0.261098671155	-0.10031108953	-0.000195461391021	0.237320931794	-0.0335051569713	0.0226524115553	0.331053927048	2.80392527886E-5	0.268968557243	-33.3111606428	-18.2133120196	44.4008098687

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 54 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 55 through 78 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 79 through 97 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 98 through 132 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 133 through 234 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 235 through 274 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1 through 21 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 22 through 39 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 40 through 78 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 79 through 112 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 113 through 132 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 133 through 189 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 190 through 234 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 235 through 250 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 251 through 273 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 0 through 97 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 98 through 207 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 208 through 273 )

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