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- PDB-9mh6: Structure of N-3 aminoglycoside acetyltransferase XIa (AAC(3)-XIa... -

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Basic information

Entry
Database: PDB / ID: 9mh6
TitleStructure of N-3 aminoglycoside acetyltransferase XIa (AAC(3)-XIa) in complex with acetylamino coenzyme A and gentamicin
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
gentamicin C1 / : / ACETATE ION / Aminoglycoside N-acetyltransferase AAC(3)-XI
Similarity search - Component
Biological speciesCorynebacterium striatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 10, 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

Downloads & links

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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)35,5496
Polymers33,4282
Non-polymers2,1224
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-24 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.372, 100.626, 39.177
Angle α, β, γ (deg.)90.000, 106.624, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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-51G / gentamicin C1 / (1S,2S,3R,4S,6R)-4,6-diamino-3-({(2R,3R,6S)-3-amino-6-[(1R)-1-(methylamino)ethyl]tetrahydro-2H-pyran-2-yl}oxy)-2-hydrox ycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside


Mass: 477.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H43N5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-6IM / acetylamino coenzyme A / (3R)-4-({3-[(2-acetamidoethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 792.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H39N8O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
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: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.37→37.54 Å / Num. obs: 53576 / % possible obs: 97.38 % / Redundancy: 3.2 % / Biso Wilson estimate: 15.39 Å2 / CC1/2: 0.998 / Net I/σ(I): 18.76
Reflection shellResolution: 1.37→1.419 Å / Num. unique obs: 5152 / CC1/2: 0.956

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→37.54 Å / SU ML: 0.1601 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 19.8372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1901 1454 2.72 %
Rwork0.1625 52099 -
obs0.1632 53553 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.66 Å2
Refinement stepCycle: LAST / Resolution: 1.37→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 139 260 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01622803
X-RAY DIFFRACTIONf_angle_d1.73613875
X-RAY DIFFRACTIONf_chiral_restr0.1035413
X-RAY DIFFRACTIONf_plane_restr0.0149493
X-RAY DIFFRACTIONf_dihedral_angle_d26.1667423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.420.29131370.27294976X-RAY DIFFRACTION93.03
1.42-1.480.28131420.23145050X-RAY DIFFRACTION94.81
1.48-1.540.22711450.19715170X-RAY DIFFRACTION96.5
1.54-1.620.19471450.18765182X-RAY DIFFRACTION97.47
1.62-1.730.23621450.18655211X-RAY DIFFRACTION97.81
1.73-1.860.23151460.17045259X-RAY DIFFRACTION97.67
1.86-2.050.19311470.1555270X-RAY DIFFRACTION98.89
2.05-2.340.17191470.14355266X-RAY DIFFRACTION98.63
2.34-2.950.1851500.15265332X-RAY DIFFRACTION99.29
2.95-37.540.16451500.15095383X-RAY DIFFRACTION99.75
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)
13.07720178709-1.75435630822-1.854350207142.622855396931.445366998174.75169206044-0.125177825910.0594305978276-0.3733783477490.002898006953550.01704217121570.1040784976850.4567519047970.009996595426420.1073041316420.157989492020.0001800850925490.01192066316490.0739424926187-0.0002453875814340.12974050357817.961558858129.637702980538.1948416384
24.866841827653.434213881965.559706001643.736536678554.848484321062.0164017115-0.09198465046321.03869993402-0.268088913152-0.5737981433270.568957882173-0.514088465653-0.624703788660.596641762567-0.4361320462310.282546847273-0.001225131218580.05908142027310.421791878958-0.05862711199150.25054467646928.016777174630.978519714930.2898269383
35.48830336205-1.95228902484-4.635839680116.050235275722.902059627292.09095754491-0.119446830104-0.24330954935-0.1254261913870.1970487833970.24776547282-0.4775222883040.04196428817230.425606211513-0.2098913014190.14673810373-0.00970804686672-0.01851852736340.232245356763-0.003355783555370.14613448672823.383997522336.964831498843.3243898584
44.39996650804-0.037895461184-0.08673831536459.015076346240.2802126041544.88704212880.0627994089094-0.188202496904-0.05614831315450.535675858192-0.0290066888548-0.03586930028950.1629129137930.00868141765408-0.07902697850590.1038301777740.003611271762030.003219464202120.09332574648730.02998694893610.058625522750913.253459306936.491580901340.592674362
51.46534952751-0.294085213933-0.319835733319.39264658801-0.6412187352670.928588644810.04304183243540.03105583033970.09278778833930.0156970200021-0.03623352785390.0312172122748-0.01593226197820.04227626916990.004010085040830.0935158524625-0.0168485246979-0.0175924844930.106517186432-0.00125404202090.070229484766812.935071889645.290537785732.4865913211
69.26194968014-3.410133165391.71809735983.14415438307-0.7526535233852.613917994490.04450481418590.63355094951-1.30410084146-0.1624423909290.08254446925910.3952364069270.979847320689-0.159928596744-0.1688035423410.358024693736-0.05434566673940.007936461122660.201845131151-0.1375426802510.3698267108429.4815575016322.150784108928.3096927726
73.42008530941-3.19760225568-2.207852050056.909188403873.12271044233.57231322464-0.0879259833837-0.02151302303-0.2361498931290.387360735559-0.01451546810010.5925683158420.260964541527-0.235809227970.1255286504230.120086454325-0.03225999481380.008737936935440.1453532497710.02076441809190.1372861544433.5933142586738.857278982534.4123949999
88.84503808612-5.18285137196-6.752817445627.9687417656.231292974822.55254793735-0.1341426576020.187672263744-0.3187755265430.03195934501740.02557153292620.1154904486950.2254519573210.02533534893250.03869241085550.1619068334110.0742492616138-0.01779920912390.1488357409730.0008101561094960.058924847224213.403039972442.779264100724.4431944003
98.368535311761.33779530963-3.448706678885.70504581381-1.547526539399.29870398926-0.2130721561310.766546590928-1.17101623623-0.3586903850130.0424008557182-0.2466386941150.460909988201-0.4010643459220.1118538009820.149417095516-0.0581585966580.004199044834850.27324282192-0.1082456916340.2504135803499.1810930496333.98390588618.8860868745
108.713547552054.8183176518-5.290564196297.38669800193-4.754418174382.172037287020.1562960341520.5791631021860.440766954188-0.0158782644228-0.02257491996980.421629884032-0.362247744827-0.708854341607-0.100176010180.1535549592640.010854313079-0.02932682745420.335064956546-0.01281564241470.1168296296748.1652528147945.745836748117.0484590851
119.73945628221.109607270658.570701300241.213620896080.7698355103837.742463334620.0335883303038-0.0581919128872-0.2099906311320.07036558975350.0206031691529-0.009090311760990.105246671973-0.166216868515-0.1545788044530.1037247203860.009105973206660.01817887503250.140450005818-0.005531015324240.092152106391924.499020157546.216271905220.4748240257
126.232707838950.190739881221.440830393992.39979414742-0.2218533177256.432500215430.07247393192790.3176659843070.4933768634640.0475221371970.0192868830244-0.0661627297216-0.494162384779-0.0424724142148-0.06125799592490.164068148548-0.006098657836480.01748711817140.08057911025750.02449442049980.2220657798818.878031390967.915315386226.7904616882
137.074762016-1.93374455161-9.095032773454.900770614274.063942038922.0011173749-0.340108763171.55680988629-0.0561964259251-0.2167269962140.2217516084720.4482344458480.20701721376-0.6418849706490.1032762673030.2892492630880.00771228289675-0.02352812432220.583654488091-0.06403745378570.4006760140066.2963348143763.34442131922.2361484012
141.820439028780.287611320597-0.1415546282852.68010942732-0.9574403593191.655362515050.04309326937550.01742476068910.2701679718130.112582937002-0.074746304620.0041080547961-0.202200328350.03984336454820.03004091175430.11625329253-0.0135200821287-0.004395683548860.0755115274949-0.01615670650950.14154905842224.460834467359.230687100928.8914446309
154.503935292910.6451727720381.634973530742.80495338524-0.6796082785345.49801497792-0.08782623550150.4119070420410.229285740806-0.2532796926060.1164358208070.00834989057202-0.272592976403-0.0361221286279-0.0260905000790.117587195752-0.002451576925760.01626020408650.1014034608170.001273330201080.11291000413425.729746866951.81580019318.6795797595
168.20771495649-0.123322674326-4.156615724050.1716035508530.1759772345732.83242239255-0.02939135210970.2111811885-0.00772445443070.0363757360218-0.0135869802435-0.03307153564550.09145243508670.003858661929960.03963358513240.1271164889220.00194962437149-0.01324635987780.1414965591280.0009832145002610.09646381599418.501564100643.156303706919.7725296911
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 45 )AA37 - 4532 - 40
44chain 'A' and (resid 46 through 58 )AA46 - 5841 - 53
55chain 'A' and (resid 59 through 83 )AA59 - 8354 - 78
66chain 'A' and (resid 84 through 91 )AA84 - 9179 - 86
77chain 'A' and (resid 92 through 107 )AA92 - 10787 - 102
88chain 'A' and (resid 108 through 120 )AA108 - 120103 - 115
99chain 'A' and (resid 121 through 129 )AA121 - 129116 - 124
1010chain 'A' and (resid 130 through 139 )AA130 - 139125 - 134
1111chain 'A' and (resid 140 through 148 )AA140 - 148135 - 143
1212chain 'B' and (resid 6 through 29 )BD6 - 291 - 24
1313chain 'B' and (resid 30 through 36 )BD30 - 3625 - 31
1414chain 'B' and (resid 37 through 106 )BD37 - 10632 - 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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