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- PDB-9mgs: Structure of aminoglycoside acetyltransferase AAC(3)-Ia in comple... -

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Basic information

Entry
Database: PDB / ID: 9mgs
TitleStructure of aminoglycoside acetyltransferase AAC(3)-Ia in complex with sisomicin and CoA
ComponentsAminoglycoside acetyltransferase
KeywordsTRANSFERASE / antibiotic resistance / aminoglycosides
Function / homologyacyltransferase 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 / Chem-SIS / Aminoglycoside acetyltransferase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHemmings, M. / Zielinski, M. / Blanchet, J. / Golkar, T. / 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 acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1463
Polymers16,9311
Non-polymers1,2152
Water1,09961
1
A: Aminoglycoside acetyltransferase
hetero molecules

A: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2926
Polymers33,8622
Non-polymers2,4304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area8450 Å2
ΔGint-39 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.213, 57.213, 125.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

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Components

#1: Protein Aminoglycoside acetyltransferase


Mass: 16931.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: aac1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D7R512
#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-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin


Mass: 447.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H37N5O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL AAC(3)-Ia with a 10x molar excess of gentamicin and CoASH in 0.1 M Tris Ph 8.5, 0.05 M MgCl2, 20% EtOH, 35% PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 10939 / % possible obs: 85.07 % / Redundancy: 21.1 % / CC1/2: 0.992 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1244 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.172 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27394 528 4.8 %RANDOM
Rwork0.22919 ---
obs0.2316 10406 85.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.357 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å2-0 Å2
2---1.16 Å20 Å2
3---2.32 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 79 61 1308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121274
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161163
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.8131745
X-RAY DIFFRACTIONr_angle_other_deg0.6561.7292670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7075153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.413512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88110178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1593.748615
X-RAY DIFFRACTIONr_mcbond_other4.163.748615
X-RAY DIFFRACTIONr_mcangle_it5.6336.695767
X-RAY DIFFRACTIONr_mcangle_other5.6296.695768
X-RAY DIFFRACTIONr_scbond_it5.2674.27659
X-RAY DIFFRACTIONr_scbond_other5.2634.273660
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.127.678979
X-RAY DIFFRACTIONr_long_range_B_refined8.82243.071442
X-RAY DIFFRACTIONr_long_range_B_other8.82842.741435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 39 -
Rwork0.266 882 -
obs--100 %

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