PDB-7jm2: Crystal structure of aminoglycoside resistance enzyme ApmA, compl...

ID or keywords:

Entry

Database: PDB / ID: 7jm2

Title

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with apramycin

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 / APRAMYCIN / Aminocyclitol acetyltransferase ApmA

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 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 apramycin
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	7jm2.cif.gz	402.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7jm2.ent.gz	290.3 KB	Display	PDB format
PDBx/mmJSON format	7jm2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7jm2_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	7jm2_full_validation.pdf.gz	1.4 MB	Display
Data in XML	7jm2_validation.xml.gz	39.1 KB	Display
Data in CIF	7jm2_validation.cif.gz	57.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/7jm2 ftp://data.pdbj.org/pub/pdb/validation_reports/jm/7jm2	HTTPS FTP

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Related structure data

Related structure data	7jm1S 7jm0 S: Starting model for refinement
Similar structure data	7jm0-d 7jm1-d 6mpr-d 5f1k-d 3kzv-1 3oic-1 4fm2-d 2bp0-2 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

95.1 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)	61.730, 107.536, 138.696
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Aminocyclitol acetyltransferase ApmA Mass: 31139.139 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-AM2 / APRAMYCIN / NEBRAMYCIN II / 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE Mass: 539.577 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₄₁N₅O₁₁ / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.46 Å³/Da / Density % sol: 50.08 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M CaCl2, 20% PEG3350, 5 mM Apramycin cryoprotectant 25% Ethylene Glycol with 10 mM Apramycin

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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: 0.9786 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.85→40 Å / Num. obs: 77441 / % possible obs: 97.3 % / Redundancy: 3.6 % / B_iso Wilson estimate: 28.08 Å² / R_merge(I) obs: 0.068 / R_pim(I) all: 0.041 / Net I/σ(I): 22.6
Reflection shell	Resolution: 1.85→1.88 Å / R_merge(I) obs: 0.691 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 3729 / CC_1/2: 0.694 / R_pim(I) all: 0.459

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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: 1.85→38.92 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2362	1971	2.58 %	RANDOM
R_work	0.1967	74411	-	-
obs	0.1978	76382	95.97 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 36.36 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→38.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6586	0	76	746	7408

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0055	6860
X-RAY DIFFRACTION	f_angle_d	0.7787	9324
X-RAY DIFFRACTION	f_chiral_restr	0.0535	1031
X-RAY DIFFRACTION	f_plane_restr	0.0049	1196
X-RAY DIFFRACTION	f_dihedral_angle_d	20.0989	2463

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 (%)
1.85-1.9	0.3947	137	0.4058	5186	X-RAY DIFFRACTION	95.02
1.9-1.95	0.5306	133	0.4448	4935	X-RAY DIFFRACTION	90.1
1.95-2	0.2679	144	0.2644	5429	X-RAY DIFFRACTION	99.57
2-2.07	0.2976	133	0.2644	5042	X-RAY DIFFRACTION	91.69
2.07-2.14	0.2742	139	0.2315	5270	X-RAY DIFFRACTION	96.83
2.14-2.23	0.2491	143	0.1974	5388	X-RAY DIFFRACTION	98.28
2.23-2.33	0.3109	132	0.2387	5067	X-RAY DIFFRACTION	91.74
2.33-2.45	0.2169	145	0.1857	5455	X-RAY DIFFRACTION	99.26
2.45-2.61	0.2484	143	0.1941	5428	X-RAY DIFFRACTION	98.78
2.61-2.81	0.2345	146	0.2086	5465	X-RAY DIFFRACTION	98.11
2.81-3.09	0.2326	146	0.191	5488	X-RAY DIFFRACTION	98.88
3.09-3.54	0.2316	142	0.1764	5372	X-RAY DIFFRACTION	96.57
3.54-4.46	0.1849	143	0.1536	5392	X-RAY DIFFRACTION	95.41
4.46-38.92	0.2026	145	0.1719	5494	X-RAY DIFFRACTION	93.86

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	1.1746329523	0.168305046297	0.620961524103	0.688195699819	-0.335246490921	0.71825614583	-0.043812824055	0.498666723712	0.243230144658	-0.4065778396	-0.0693347789266	0.1314212858	0.104481745285	-0.0620208425688	0.000983302805857	0.417113021594	0.0176405411252	-0.100213526387	0.322771070908	-0.0467458517654	0.347945972905	-3.25799029614	-14.7827312023	-31.1099421164
2	2.37066858068	0.472529323532	-0.07998923187	2.10733380816	0.619675123273	1.27064797023	-0.0261646829402	-0.207067846128	-0.179497273345	0.0351576710056	-0.104392021886	0.487321887483	0.167875251916	-0.200443301324	-4.60221807968E-8	0.453614059807	0.00258461570695	-0.078465680477	0.313608454159	-0.0732216012416	0.39287624246	-8.51904113812	-19.4074763781	-23.2466891882
3	0.46875523891	0.204612430099	0.237192613654	0.383031735869	-0.136814454125	0.284887390099	0.0941195036713	0.148210253848	-0.0250823337581	-0.422845936695	-0.277917996837	0.268734687616	0.0365818441046	0.0545404699798	5.68065228599E-8	0.454674916352	0.0533982003226	-0.0894027948176	0.285048814127	-0.0690338257938	0.291277751678	9.09880645271	-15.6022930088	-28.0455993126
4	0.810628154547	0.2526698558	0.604788714222	0.609917268602	-0.173223837969	0.720766132438	-0.00785897977219	0.124467577571	0.0963801196004	-0.381597961217	-0.111260821191	0.223208552743	-0.00656222550464	0.0914088142902	-0.000121713998396	0.308472981229	0.0615760127099	-0.0415121489955	0.217202310756	-0.0283352703912	0.183493689659	15.8123444713	-11.3042503595	-23.2304124037
5	0.83456509776	0.177657407302	0.0191004639163	3.23635277576	-0.984683243069	0.32187574095	-0.00511229112522	0.0715071320854	0.12294102962	-0.194930215018	-0.136862890651	-0.321613462777	0.0961926034554	0.257346994226	0.000325531634121	0.27103514312	0.0339027513701	0.0163662772942	0.286262195481	0.0244155905012	0.240447461124	26.2095311239	-2.14345537258	-24.0550996617
6	0.570069921827	-0.783167953916	0.0743268765678	1.18309632489	-0.244915133542	0.832039522603	0.0290703825856	0.0620893778125	-0.434437260026	-0.304995346208	-0.160103054178	-0.276945785857	0.471589062597	0.244359306875	4.84270356556E-8	0.488712497617	0.139608092102	0.0293670214446	0.307491080085	0.0125005727004	0.397543667652	25.2440250409	-33.2559514235	-19.1268446039
7	1.47325498248	0.257892278217	0.119768818024	0.668911598143	0.241400602494	0.72219815132	0.145890749191	-0.323281490994	-0.293966604983	0.164863828827	0.0785955393749	0.309227042677	0.574676439024	-0.193082523178	0.00112663844833	0.286099945178	-0.0500366979455	0.00436345153419	0.380023837055	-0.0120441535479	0.386515257894	-15.4068767104	-3.11008697602	-0.754186850515
8	0.0847203262026	-0.131906343822	-0.0518754325831	0.13751261997	0.0734415080799	0.32946976087	0.0977926655936	0.418104886776	-0.768735454294	-0.178670772233	-0.146364560343	0.626144797502	0.426373684703	-0.281983424914	-1.84974209833E-7	0.381756537685	-0.0405837157614	0.0223684990587	0.361920461111	-0.0788647607628	0.470026011894	-16.996518151	-6.17374252126	-10.9447624673
9	0.890291451152	0.271135871985	0.667069600218	1.03556915178	-0.343351554525	1.20195925497	0.00620756627046	-0.0113692331273	0.625105889219	0.121517763502	0.0158852681863	0.171711356043	-0.584153897491	-0.0815437507342	2.95000277495E-8	0.322112516863	0.0333412714683	0.00199076144921	0.336013508811	-0.00855447949659	0.464909482512	-14.949786778	8.71889707378	-5.67277742758
10	0.805677082186	0.185051721088	0.348516219441	0.366340905104	0.255593818398	0.21590959306	0.0398667806712	0.151401257557	-0.0756491236861	-0.0818607026821	0.0676968603153	0.214454195742	0.269184534814	0.199420363966	-1.79797311855E-5	0.221929392785	0.035264971924	-0.00284565249305	0.328231259111	-0.0617781025274	0.314404010511	-5.47230646336	-3.33185417396	0.272797690996
11	0.892362468632	0.241994094548	-0.0120741880775	0.452222951688	0.420086691733	0.367878113218	-0.0168208834971	0.055365666987	-0.118986301627	-0.0959849184444	-0.147232085497	0.19171521123	0.227556637008	-0.205827253992	-1.55332260311E-7	0.288669695428	0.0379460394044	0.00592632732818	0.283127813318	-0.0432862076366	0.209521075787	2.86465224661	-8.76880350817	1.98611757941
12	1.18650379801	-0.91137224872	-0.667465545818	1.26121547808	1.39223130641	1.06296778126	-0.140162539363	-0.13207293355	-0.243428268488	0.237476879538	0.0732925743856	0.186484355661	0.348579462537	0.117542599304	-6.06823546031E-5	0.361752910202	0.0675980524752	0.0100701483251	0.256780914577	0.0218027918472	0.212531251709	12.8781784015	-19.4581675266	-4.0034938122
13	0.802953165391	-0.152912955268	-0.258997047634	0.940966771934	-0.115883815606	0.598898720554	-0.0330258246537	-0.32926937719	0.14874274537	0.0432303643188	-0.00541242036029	-0.544300713253	0.0456304795687	0.382792673191	-0.0169903732338	0.300974595063	0.0743412634358	-0.037169281657	0.377469533918	-0.0544003360832	0.211596394061	19.0672698824	-4.46689798339	6.37373233771
14	2.89533492102	1.91606910637	-0.8245094435	3.54486039517	0.41838671605	0.690249539978	-0.0385330207416	-1.21812789087	-0.498059616923	1.44175194978	-0.00460382485564	-0.596833038233	0.281340622822	0.155219205096	0.0387592283941	0.610461858167	0.0994769314317	0.0554200282049	0.518768264913	-0.110502305534	0.176319955792	9.62605364421	-0.37683523031	21.4771982609
15	0.650807032649	0.101411637103	0.354573670227	0.709490708294	-0.221815061276	0.440205914379	-0.272872075353	-0.726807232781	0.499743341586	0.913875443351	0.136494159718	0.0707226460297	-0.184881117919	-0.18201143559	0.00241024443716	0.507964490072	0.0776369803531	0.0309903463205	0.602172145304	-0.159150886815	0.357572296726	5.6467495728	8.75918589965	23.5540554949
16	1.33811250907	-0.0432935162115	-0.555884067997	0.477093252733	-0.202976056604	0.680740962399	-0.0731969000912	-0.0901661639781	0.726613104824	0.0330751049224	0.129115857791	0.379668514567	-0.133549136968	-0.440221498762	-0.00657769493209	0.315532106107	-0.010603778549	-0.0842544079441	0.340583058255	0.0794049791541	0.510084446767	-5.78115093285	15.2610405681	-26.3583157201
17	1.67535026382	0.675671911359	0.502957722942	1.51973221459	-0.475720507187	2.09109348424	-0.048490295593	0.602467640089	0.0081771568847	-0.340172458279	0.0953552148092	-0.0450157587981	0.156981841157	-0.061167579827	1.20599580204E-7	0.361647082944	0.00142484315475	-0.0758369323217	0.38909832087	0.0893687290951	0.428859219584	-3.44804660971	9.20687407997	-34.9970422215
18	0.443767176121	-0.233382258728	0.368787678194	0.212256921404	-0.234624034237	0.503746907689	-0.0756173695552	-0.0160088579765	0.58494204022	0.128281811428	0.396617343438	0.453817240043	0.0755549507021	-0.266904201452	9.85975215837E-5	0.290398855497	0.025120879238	-0.0618091816402	0.320983427991	0.0777335098548	0.526233921078	5.65828774171	17.6119701277	-20.9172992213
19	0.661729714202	-0.354904295334	0.195915040149	0.26351843207	0.11923198031	0.793267358541	0.0271921544502	-0.0721896922011	0.293110670361	0.069575928013	0.0754381311958	0.351850867032	-0.0809664020351	-0.117042609625	3.9871793808E-7	0.209850077232	0.00580886704821	-0.00541834764217	0.245830429403	0.000746650983242	0.335703230137	11.9889790473	14.0705367481	-15.0914086095
20	1.27291666149	0.475454501668	-1.03097613525	0.476698372706	-1.09563211994	1.69307252671	0.0861760995168	-0.256298974154	0.453024550212	0.185687775153	0.0578895435588	0.0969463354601	-0.238662033742	0.0850052148226	8.64405374454E-5	0.252724236019	0.0182986245421	-0.0129063020729	0.299729593799	-0.118485205692	0.340252837569	11.9568614589	14.4498134509	1.45082725342
21	1.85652997351	0.119891493638	-0.152319619893	1.52981540105	0.313134314581	1.45698864953	-0.0522063322006	0.0344245301629	0.54187427484	-0.145755666419	-0.0682832660879	-0.257119151204	-0.110438988538	0.511098890955	-0.00379311302643	0.191177403886	-0.0411586264505	-0.0344627988122	0.301373721393	0.0107990357689	0.448775749562	28.9860168191	20.1552382321	-21.8987680432

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 78 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 97 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 98 through 132 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 133 through 234 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 235 through 272 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 21 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 22 through 39 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 75 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 76 through 93 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 94 through 119 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 120 through 189 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 190 through 234 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 235 through 250 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 251 through 273 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 32 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 33 through 78 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 79 through 97 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 98 through 132 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 133 through 207 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 208 through 272 )

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