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

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Basic information

Entry
Database: PDB / ID: 7uuk
TitleCrystal structure of aminoglycoside resistance enzyme ApmA, complex with tobramycin
ComponentsAminocyclitol acetyltransferase ApmA
KeywordsTRANSFERASE / 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 / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologyTrimeric LpxA-like superfamily / transferase activity / metal ion binding / TOBRAMYCIN / Aminocyclitol acetyltransferase ApmA
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Bordeleau, E. / Wright, G.D. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance.
Authors: Bordeleau, E. / Stogios, P.J. / Evdokimova, E. / Koteva, K. / Savchenko, A. / Wright, G.D.
History
DepositionApr 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Other ...Data collection / Other / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / pdbx_SG_project / pdbx_initial_refinement_model / struct_keywords
Item: _audit_author.name / _pdbx_SG_project.full_name_of_center ..._audit_author.name / _pdbx_SG_project.full_name_of_center / _pdbx_SG_project.initial_of_center / _struct_keywords.text
Revision 1.2Nov 29, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminocyclitol acetyltransferase ApmA
B: Aminocyclitol acetyltransferase ApmA
C: Aminocyclitol acetyltransferase ApmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4829
Polymers93,9733
Non-polymers1,5096
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-87 kcal/mol
Surface area34790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.146, 107.405, 134.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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

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Components

#1: Protein Aminocyclitol acetyltransferase ApmA


Mass: 31324.320 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-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL / Tobramycin


Mass: 467.514 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H37N5O9 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M calcium chloride, 20% PEG3350, 5 mM tobramycin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.82→30 Å / Num. obs: 21504 / % possible obs: 96.4 % / Redundancy: 5 % / Biso Wilson estimate: 44.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.078 / Net I/σ(I): 5.9
Reflection shellResolution: 2.82→2.87 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 1002 / CC1/2: 0.655 / Rpim(I) all: 0.389 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JM2

7jm2


Resolution: 2.82→29.85 Å / SU ML: 0.3761 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.7087
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 1072 5 %RANDOM
Rwork0.1965 20369 --
obs0.1994 21441 95.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.62 Å2
Refinement stepCycle: LAST / Resolution: 2.82→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 99 195 6886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416887
X-RAY DIFFRACTIONf_angle_d0.66019357
X-RAY DIFFRACTIONf_chiral_restr0.04791030
X-RAY DIFFRACTIONf_plane_restr0.00491205
X-RAY DIFFRACTIONf_dihedral_angle_d16.93732550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.950.33121230.2732352X-RAY DIFFRACTION90.63
2.95-3.10.31911370.26012573X-RAY DIFFRACTION97.94
3.1-3.30.34111340.24332549X-RAY DIFFRACTION97.49
3.3-3.550.28291340.21232560X-RAY DIFFRACTION97.5
3.55-3.910.2561370.18022583X-RAY DIFFRACTION97.42
3.91-4.470.2151340.16042573X-RAY DIFFRACTION96.68
4.47-5.630.19961360.15972575X-RAY DIFFRACTION95.59
5.63-29.850.22941370.19452604X-RAY DIFFRACTION92.63
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.34349979536-0.376334292463-0.1844168397214.35539689060.01283403406822.10869343223-0.1738025740361.08435186080.283094313-0.229607598294-0.1321045311020.4120836913810.5240768728020.1010047271320.2418152443170.54804494945-0.0168778181971-0.03455017431850.46683449237-0.02642544996980.310107813855-3.06896534433-19.2717708938-30.4670132253
25.910821437732.48990094820.4164641864216.02381351457-1.379906963414.26470816593-0.1184412399180.463496144920.84817827291-0.5184685090790.1189741988691.13694460929-0.00952553093607-0.319472214712-0.01601663838710.3699137894880.0323136152659-0.08311188437150.378248164899-0.03114825939010.538255265308-10.7489668266-14.190905642-29.100757499
39.73481976571-3.20356125273-0.2512838489835.535790715511.780223735938.07025826606-0.0525016051454-0.620100781752-0.5640181338030.802647498240.4581757396910.1941232275730.5452095740860.074640365003-0.3247375392390.486649090373-0.1057020812550.03749920500120.386428886111-0.009143074483770.333946029632-7.13429809144-19.9040168684-18.7611068426
43.484419015342.4744498133-0.1613513902054.1783162137-0.1980681116870.859783607104-0.1091617861440.1660911121080.186965971327-0.04947078268730.3310286137120.209518466354-0.1839636258050.345946633752-0.2656215873990.5846861199460.0331624319254-0.04903744372840.4078762395520.03396860150330.2660843622118.29928571416-16.776908391-25.1086529534
53.309377865381.70263109466-1.029343428437.613024267280.9949851584053.28461433737-0.306093594577-0.0740124695820.230006790834-0.1185358590730.324836774810.233887302070.004448113669990.27440159257-0.02777009616720.3380576255110.0456523431948-0.06383928688030.2870513481740.001597348199780.29856195130216.3397721379-9.39005097223-22.5433122845
60.72540375097-0.08343920274620.8131809103887.51677113074-1.974896498791.89019363573-0.08147184344260.009854958181010.0970404442884-0.496403136937-0.0702650717169-0.4083166584790.04636109490180.1555811220310.1320376210830.321267272873-0.01556516597320.02421974994040.3299648527090.005374835878090.2680434828324.6193345071.12024349949-26.1814310284
73.91499362588-2.25939166371-0.9819908507545.45385877935.062574733645.130045075220.1657713541970.0127880373968-0.129702341987-0.08070918950410.262787847031-0.282030443315-0.3614596281810.95287588293-0.4224234818850.582333348064-0.0297614073230.004607351288340.2847551980470.08154348429540.52745149019929.9645028507-12.1891805361-13.9157549038
85.671433642491.079776084422.37499850885.115136345160.7841217945937.87467069141-0.273751333592-0.172483297808-0.5205525897970.226055198455-0.117220684242-0.6974163534160.6106004504920.6228374450390.2851757902160.4318150045940.0793432250854-0.002463080102510.3577014750620.2130408885260.46288643875532.2651678919-24.3702684119-14.7097979623
95.83374286076-0.9252654723681.223612796555.94344273428-1.090772387866.750647240090.0993900928030.17090218956-0.663005660181-0.101809882513-0.292461728398-1.165073861890.345531576075-0.2729342863040.1274353014750.4801070342260.0320503714684-0.057880568660.360402855244-0.01030429414150.52458246298722.6233294331-35.3550687784-18.4364740631
105.396853912350.07304601083651.541356419973.264627354070.005779255716264.68546536855-0.04719972076010.200972779020.852355048548-0.316415169286-0.0868040048413-0.1005006921980.0432191637695-0.6335233050180.1479168392420.4055635131240.04160171774410.08209971234140.4107373158210.09874401322410.465807096006-7.3898385121114.1726508078-28.5075203415
113.327345906021.26454216621-1.739521186553.961355655923.372959901355.59622534403-0.1231548229670.215159701393-0.0496673984156-0.224469982009-0.00403650580025-0.6014949502130.4783054778040.7728438548670.2062457767580.5654441406110.0423259082767-0.04757589950740.5181829917050.1075548715790.4415912486360.01817702591887.05824841327-34.2380560513
125.04051324602-0.4015303634392.102873959311.07863031831.121308959164.66797958256-0.209338088591-0.312858423370.475390386081-0.1297790707930.4519459594460.443945060923-0.45991222405-0.0944171588403-0.06320811789750.3651043748040.154584947191-0.02949420278680.4153620774270.1754898222880.3152638285684.5241384064915.1731308459-22.5095362862
132.750220671430.325116859856-2.931194381351.79255048711-0.4017227595238.66413539647-0.03287647447470.08183529512650.06832194720260.001432370507210.01479597067280.0537005627873-0.0899180052049-0.24598606408-0.02985996847810.1984526488860.0331939421346-0.004948679873390.2658630096040.0190200984560.37212488912711.588483586614.4015969785-14.0419913351
141.156797898140.477282194891-2.022414350731.41368238642-1.05158506164.533447076680.0685566574866-0.1340778240840.2279235668070.1491176651730.01545295537710.034122661599-0.3468865116080.20341555834-0.07898189471910.2803726370310.0091743059275-0.07157936551160.294837008627-0.05273133415190.36041437862718.371757405415.9292540583-5.74753205322
151.80926436362.700640814292.537564156525.144623822753.485184247725.17311795119-0.3391069012870.4847062173560.7392796362740.438796235379-0.1825947523250.4576694943170.03332880155841.27046721580.6862918891770.420587694338-0.01074753698120.05971404467340.4392567001910.177473488580.56845232670433.584484537124.1444501342-30.1751891273
162.62873289554-1.248820921350.5293556732580.9229520550291.047701290854.652383297090.0555883890521-0.0770655830246-0.633039095769-0.0844355087173-0.09540684553120.4920454261180.258367687615-0.2596762920910.04030265565720.395578555477-0.07316216897640.0108599452640.343002913793-0.01505874328320.581643429351-17.4885450581-2.67123472279-4.85880595541
173.4422466047-2.7587995872.493707421426.93153264391-3.128686476275.189705601290.16822696914-0.00728374520850.131861561388-0.190883069666-0.289756595399-0.001202603244140.09604914798530.1678575762240.09940542835040.262809579258-0.0459890858471-0.01196386479980.34301433925-0.01333438210770.269064665678-9.999520470053.8038532995-2.57856614683
181.54954404921-2.54287905221-1.946195982685.196953872973.976032517823.71323889554-0.24253940522-0.0979129850691-0.2580239368980.5423496260620.1417402182720.1728307535170.3494059814380.3002985014290.1172488858450.3762592321240.04403475486990.01460289734860.3245962700090.04195166502490.29438847154410.64252238-15.7638914543-0.911913960874
191.80894695051-0.1529617034730.8904362994021.7900856067-0.5333340963171.0404367826-0.234988593592-0.4998141720120.3736716938010.6417861873580.184880145071-0.1970487265630.2655001094340.2091433362450.05741557218070.5225961544590.0416551517763-0.07996510663280.472248150266-0.05765207639320.31492145301511.99417107381.194358070318.432068549
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 21 )AA2 - 211 - 20
22chain 'A' and (resid 22 through 47 )AA22 - 4721 - 46
33chain 'A' and (resid 48 through 75 )AA48 - 7547 - 74
44chain 'A' and (resid 76 through 104 )AA76 - 10475 - 103
55chain 'A' and (resid 105 through 132 )AA105 - 132104 - 131
66chain 'A' and (resid 133 through 212 )AA133 - 212132 - 211
77chain 'A' and (resid 213 through 226 )AA213 - 226212 - 225
88chain 'A' and (resid 227 through 244 )AA227 - 244226 - 243
99chain 'A' and (resid 245 through 274 )AA245 - 274244 - 273
1010chain 'B' and (resid 1 through 47 )BB1 - 471 - 47
1111chain 'B' and (resid 48 through 75 )BB48 - 7548 - 75
1212chain 'B' and (resid 76 through 93 )BB76 - 9376 - 93
1313chain 'B' and (resid 94 through 132 )BB94 - 13294 - 132
1414chain 'B' and (resid 133 through 256 )BB133 - 256133 - 256
1515chain 'B' and (resid 257 through 274 )BB257 - 274257 - 274
1616chain 'C' and (resid -1 through 47 )CC-1 - 471 - 49
1717chain 'C' and (resid 48 through 93 )CC48 - 9350 - 95
1818chain 'C' and (resid 94 through 207 )CC94 - 20796 - 209
1919chain 'C' and (resid 208 through 274 )CC208 - 274210 - 276

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