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- PDB-9mh5: Structure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) ... -

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Basic information

Entry
Database: PDB / ID: 9mh5
TitleStructure of N-3 aminoglycoside acetyltransferase XI (AAC(3)-XI) in complex with coenzyme A and acetylated sisomicin
ComponentsAminoglycoside N-acetyltransferase AAC(3)-XI
KeywordsTRANSFERASE / antibiotic resistance / aminoglycosides
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / COENZYME A / acetylsisomicin / Aminoglycoside N-acetyltransferase AAC(3)-XI
Similarity search - Component
Biological speciesCorynebacterium striatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsZielinski, M. / Hemmings, M. / Golkar, T. / Blanchet, J. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-162365 Canada
CitationJournal: Commun Chem / Year: 2025
Title: Enzyme-mediated aminoglycoside resistance without target mimicry.
Authors: Hemmings, M. / Zielinski, M. / Golkar, T. / Blanchet, J. / Pistofidis, A. / Munro, K. / Schmeing, T.M. / Bohle, D.S. / Berghuis, A.M.
History
DepositionDec 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside N-acetyltransferase AAC(3)-XI
B: Aminoglycoside N-acetyltransferase AAC(3)-XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4945
Polymers33,4282
Non-polymers2,0673
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-29 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.489, 100.555, 39.340
Angle α, β, γ (deg.)90.000, 106.550, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Aminoglycoside N-acetyltransferase AAC(3)-XI


Mass: 16713.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium striatum (bacteria) / Gene: CBE89_03745 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K2X0F2
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DVM / acetylsisomicin / N-[(1S,2R,3R,4S,5R)-5-amino-2-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-4-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]acetamide


Mass: 489.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H39N5O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium acetate pH 4.6, 10-45% (v/v) 2-methyl-2,4-pentanediol, 0-20% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.46→50.28 Å / Num. obs: 44823 / % possible obs: 97.72 % / Redundancy: 5.3 % / Biso Wilson estimate: 18.82 Å2 / CC1/2: 0.995 / Net I/σ(I): 23.14
Reflection shellResolution: 1.46→1.512 Å / Num. unique obs: 4291 / CC1/2: 0.982

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→50.28 Å / SU ML: 0.1507 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 17.7557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1768 2191 4.9 %
Rwork0.1535 42540 -
obs0.1546 44731 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.42 Å2
Refinement stepCycle: LAST / Resolution: 1.46→50.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 133 194 2558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212684
X-RAY DIFFRACTIONf_angle_d1.38243712
X-RAY DIFFRACTIONf_chiral_restr0.0914407
X-RAY DIFFRACTIONf_plane_restr0.0109485
X-RAY DIFFRACTIONf_dihedral_angle_d20.4848411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.25091470.20632545X-RAY DIFFRACTION95.26
1.49-1.530.26451350.18092566X-RAY DIFFRACTION93.95
1.53-1.560.22131410.17322561X-RAY DIFFRACTION95.17
1.56-1.610.22341530.16812617X-RAY DIFFRACTION96.25
1.61-1.650.19521370.16782594X-RAY DIFFRACTION97.29
1.65-1.710.20971350.16732689X-RAY DIFFRACTION97.82
1.71-1.770.2261280.17412697X-RAY DIFFRACTION98.5
1.77-1.840.16911360.16112632X-RAY DIFFRACTION98.37
1.84-1.920.181310.15282678X-RAY DIFFRACTION98.25
1.92-2.020.19261270.14642669X-RAY DIFFRACTION97.69
2.02-2.150.18411220.14582716X-RAY DIFFRACTION99.16
2.15-2.320.14611350.13612728X-RAY DIFFRACTION99.41
2.32-2.550.17871420.14252693X-RAY DIFFRACTION99.44
2.55-2.920.1871570.15012700X-RAY DIFFRACTION99.51
2.92-3.680.14511260.15072713X-RAY DIFFRACTION98.54
3.68-50.280.17221390.15682742X-RAY DIFFRACTION99.04
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)
13.08321774078-1.0271948596-1.769431815052.369042179850.7827349713774.87717699455-0.1097935555120.00166859702049-0.2956319613090.02182747755970.01953829820070.146022850370.380623005023-0.01929190058630.1383262356540.186800205022-0.001572638305420.008796092874730.1142045948610.004184896762940.17523437021517.532781998529.79559134438.6519326266
27.122734896834.54410480455.725965857564.799484229654.458527504127.80079057395-0.2889215169840.914710947008-0.100913892208-0.8796877565480.506617782587-0.516647771562-0.9422252371960.472287289172-0.05056111964050.3306319586920.007036594715770.05476401196020.351417056184-0.0465014082560.26805743990828.096315497230.988581121830.0966006462
38.78516653093-2.179802059570.4460793966295.853183034930.6267403232555.10051933917-0.04328775561110.0660117670576-0.1719501495750.1189962953190.146261007738-0.1460886396920.09076089641760.287328414134-0.1332272592470.199788845556-0.0220719573317-0.002034158497220.190141264278-0.0003836043381760.12758204415822.574386600337.455004815443.5463127669
43.69571416926-0.409994468434-0.3608271127835.80467997241-0.2386406462823.463824965050.016798548272-0.204731825250.01713303037180.472891909369-0.0684073017404-0.1814019501220.03342385677460.1255041357610.03864122575920.134064835248-0.0134160659168-0.007287385470380.1282070544140.004113506450120.086226113472913.83277961538.454396687738.2869722409
51.800206538590.34335464097-0.2726115605369.4500529674-0.3413758216220.694460521644-0.00920321167422-0.01206861726560.1493220128260.04161003712520.07191537478270.0009819152087730.0436880000213-0.0180545167375-0.05573737025920.142791585773-0.0136390622259-0.01569564021980.161419076543-0.005728426071540.10833566162312.608967355246.500947575831.2985143035
63.28316230493-0.462132540186-0.01445645210397.670102606970.7573088190492.60502844002-0.09748819818090.196877218758-0.3904097156790.07191563907650.09256413208430.4114813864090.355846829058-0.2926772291730.03092368653920.142503677285-0.05825424216520.008462462599130.159759371963-0.01120653276680.143246463385.990087698932.372776571531.7982378619
74.42895592751-0.634113465467-2.059777923483.168349446260.3826220765832.5906565216-0.0690283636390.392353694397-0.240578080463-0.135684809426-0.0414460787838-0.08004836393980.235255903135-0.3091866633350.09952502545190.115146339339-0.0185331657757-0.01326655954340.153142982985-0.01119900920610.095118322623812.178738587738.697389149722.4872180638
86.494968998282.3819955952-4.208500525355.22184536538-2.376227176226.970661458530.1280725237590.9001576036750.777569457655-0.3040309191220.06575469164920.531896991988-0.424457422646-0.864628601402-0.217015806230.1518206247420.0535608585531-0.03634452034740.3902232580440.02989703095110.1828399741278.2323227912245.623333205817.1350184062
99.148309247431.057494499577.077827379531.675387289680.2338183647366.914574003370.0711604994511-0.0915989348399-0.238027349105-0.02755615617950.0130487708972-0.04951204776890.12414552392-0.0733068722228-0.1116761390370.1270879888060.01653255358090.02368960194810.148240332958-0.003011321138470.10974888965224.615664201846.169564480320.5829845216
102.576476738410.820795902345-1.610210381951.19631358243-0.06749983812912.20905710279-0.02940730117530.2029018061660.495658737752-0.0671151983260.0002402679432640.0486111752548-0.645867329828-0.07864682552270.00603676343630.2341922444760.00504607979142-0.01793219581720.1323890578710.005991770815660.30046454163719.436561636668.400966586127.2067438597
113.13744218412-0.290840965429-4.041098917452.425421897692.349712286019.42606189443-0.7584889981871.55955133369-0.417331437738-0.125612747163-0.0522284676350.7947944071880.101618673714-1.110741466280.6050413601090.384828033325-0.0480683583840.02526360699820.839859209058-0.1785300606690.6274308201457.4209680725863.089748457521.4935155386
126.726387224251.121231363660.2437028955915.149586899972.151694177073.843760201020.260891358709-0.4176895451240.4312832671620.435928499216-0.07241336116420.2299517619660.057252415723-0.0702982272504-0.1822356514530.242783725387-0.002899741991560.02130043055360.167310613719-0.07697209145360.30876289331614.457365986264.00839580536.7020613127
132.004100280960.554374992512-0.2808757818584.4053468181-2.608596625632.921391962340.02041266116380.08570835967690.2182008238040.007611536827350.001925862778340.19418927007-0.1486710391170.00588142731237-0.04610933457820.115758467609-0.00806576816848-0.01255958621290.0920662532052-0.02150194360560.14771666082224.083910798958.251464560627.3921394559
142.72362546984-0.389585320911.256729570346.48567110874-5.423997368877.46879861526-0.0851725746380.01155850987320.2263602635810.350637297408-0.286892315013-0.536911716933-0.3519967973790.4602953588170.4273626794410.151072365681-0.0367620939294-0.01891959257160.1482029655070.01918867132690.2236127230232.981944761158.733666445228.1740962411
153.158270493090.3642796774760.7075688785112.40305364795-1.030177848635.5534655195-0.04060806656550.2516559170630.16408322592-0.1834423938480.0842106947181-0.00239822097662-0.224369390313-0.084018132081-0.04345808218170.1537715672340.004246713193310.006520534876630.1364599984250.003541012947920.15886661840625.43154196351.689330581119.2783102046
166.2887227110.770364253199-3.16090293660.275017681166-0.3980131997812.11520461120.0118568499640.150514156810.0469431231245-0.0125828849077-0.0517517300441-0.01779926835740.0553169264914-0.02756012528570.01827009720870.1431749453340.00521813748025-0.01531422088230.186866986315-0.0005663129524710.10111160758118.89635949742.666953024519.9183017289
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 28 )AA6 - 281 - 23
22chain 'A' and (resid 29 through 36 )AA29 - 3624 - 31
33chain 'A' and (resid 37 through 46 )AA37 - 4632 - 41
44chain 'A' and (resid 47 through 66 )AA47 - 6642 - 61
55chain 'A' and (resid 67 through 83 )AA67 - 8362 - 78
66chain 'A' and (resid 84 through 106 )AA84 - 10679 - 101
77chain 'A' and (resid 107 through 129 )AA107 - 129102 - 124
88chain 'A' and (resid 130 through 139 )AA130 - 139125 - 134
99chain 'A' and (resid 140 through 148 )AA140 - 148135 - 143
1010chain 'B' and (resid 6 through 28 )BD6 - 281 - 23
1111chain 'B' and (resid 29 through 36 )BD29 - 3624 - 31
1212chain 'B' and (resid 37 through 47 )BD37 - 4732 - 42
1313chain 'B' and (resid 48 through 91 )BD48 - 9143 - 86
1414chain 'B' and (resid 92 through 106 )BD92 - 10687 - 101
1515chain 'B' and (resid 107 through 130 )BD107 - 130102 - 125
1616chain 'B' and (resid 131 through 148 )BD131 - 148126 - 143

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