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

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Basic information

Entry
Database: PDB / ID: 9mgt
TitleStructure of N-3 aminoglycoside acetyltransferase XIa (AAC(3)-XIa) in complex with coenzyme A and tobramycin
ComponentsAminoglycoside N-acetyltransferase AAC(3)-XI
KeywordsTRANSFERASE / antibiotic resistance / aminoglycosides
Function / homology: / acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / COENZYME A / TOBRAMYCIN / Aminoglycoside N-acetyltransferase AAC(3)-XI
Function and homology information
Biological speciesCorynebacterium striatum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 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)35,4305
Polymers33,4282
Non-polymers2,0033
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-32 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.179, 101.598, 39.828
Angle α, β, γ (deg.)90.00, 106.11, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: 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


Mass: 467.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37N5O9 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
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: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Apr 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→32.07 Å / Num. obs: 19238 / % possible obs: 99.17 % / Redundancy: 18.5 % / Biso Wilson estimate: 15.82 Å2 / CC1/2: 0.998 / Net I/σ(I): 18.58
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 1900 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→32.07 Å / SU ML: 0.1654 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.469 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1877 1270 6.64 %
Rwork0.1433 --
obs0.1462 19127 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.78 Å2
Refinement stepCycle: LAST / Resolution: 1.96→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 128 276 2620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772495
X-RAY DIFFRACTIONf_angle_d1.13243424
X-RAY DIFFRACTIONf_dihedral_angle_d11.947362
X-RAY DIFFRACTIONf_chiral_restr0.048386
X-RAY DIFFRACTIONf_plane_restr0.008430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.040.20651380.15921939X-RAY DIFFRACTION98.3
2.04-2.130.20521370.14831979X-RAY DIFFRACTION98.83
2.13-2.240.20291410.13571965X-RAY DIFFRACTION98.78
2.24-2.380.20521430.13811987X-RAY DIFFRACTION98.98
2.38-2.570.19821400.14311973X-RAY DIFFRACTION99.39
2.57-2.830.20151420.14982010X-RAY DIFFRACTION99.35
2.83-3.230.19721420.14461978X-RAY DIFFRACTION99.72
3.24-4.070.15391410.12931998X-RAY DIFFRACTION99.53
4.08-32.070.17741460.15042028X-RAY DIFFRACTION99.82
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)
12.4457-1.4647-1.75032.3618-0.9444.62390.27140.36890.2606-0.09320.05150.1038-0.2671-0.609-0.2690.20170.03160.01040.15120.04320.217716.349166.789525.194
23.98871.63850.51114.64320.23135.71370.294-0.2970.32370.37430.1490.1359-0.3451-0.1935-0.35910.19280.0080.03650.0896-0.03230.220914.472563.848235.4218
31.4487-0.4981-0.25886.4946-1.73812.4470.0035-0.04540.08680.33030.01410.1431-0.2249-0.0279-0.03210.0548-0.0283-0.00080.0728-0.02310.080124.111254.830631.9598
42.094-0.15450.21224.194-2.35943.8102-0.02430.11430.2605-0.0077-0.0223-0.1534-0.3306-0.0050.03520.1138-0.00020.01190.05180.01080.099428.148160.250923.5207
52.99580.43811.52621.77840.16513.6712-0.07720.32220.1831-0.30230.11080.0669-0.1739-0.1184-0.05580.09980.0076-0.01190.11040.03950.149525.348351.568218.0229
64.90260.4897-2.3640.1261-0.37231.5945-0.04360.11660.03930.0236-0.0135-0.02270.1508-0.02580.04170.0846-0.0046-0.020.1283-0.01520.052218.59342.559819.3175
71.5028-0.215-0.0732.50721.14693.32540.01450.0888-0.43530.04060.068-0.16120.27620.28-0.04750.12770.02570.00010.1074-0.03010.167120.909531.569738.1581
84.8583-0.1713-0.16072.3251-0.54924.24050.0516-0.24060.03280.59520.0286-0.21520.0723-0.0249-0.08530.1446-0.0082-0.00050.0886-0.00060.097213.316736.69740.5646
92.189-0.2767-0.10233.96340.06051.4517-0.09750.0714-0.00810.06810.09110.12940.1403-0.0991-0.02870.0746-0.0246-0.00810.0885-0.00810.04159.757940.124231.8769
102.420.0110.19740.3708-0.18272.944-0.17090.3153-0.1944-0.0809-0.0920.07040.4538-0.3526-0.07950.0934-0.0654-0.02050.2371-0.07480.089611.034336.555218.8502
115.52522.51792.29253.18121.61125.0338-0.0970.08050.1406-0.09730.08470.2267-0.0081-0.3866-0.05520.10010.00070.02770.10930.03730.074821.823246.479418.4226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 130 )
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 148 )
7X-RAY DIFFRACTION7chain 'B' and (resid 7 through 45 )
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 58 )
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 113 )
10X-RAY DIFFRACTION10chain 'B' and (resid 114 through 135 )
11X-RAY DIFFRACTION11chain 'B' and (resid 136 through 148 )

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