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

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Basic information

Entry
Database: PDB / ID: 9mgu
TitleStructure of aminoglycoside acetyltransferase AAC(3)-Ia in complex with 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 / Aminoglycoside acetyltransferase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.34 Å
AuthorsHemmings, M. / Blanchet, J. / Zielinski, M. / 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)17,6992
Polymers16,9311
Non-polymers7681
Water52229
1
A: Aminoglycoside acetyltransferase
hetero molecules

A: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3974
Polymers33,8622
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7840 Å2
ΔGint-41 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.459, 57.459, 123.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 295.15 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: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.34→28.9 Å / Num. obs: 8695 / % possible obs: 92.84 % / Redundancy: 8.4 % / Biso Wilson estimate: 30.39 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.22
Reflection shellResolution: 2.34→2.67 Å / Mean I/σ(I) obs: 1.98 / Num. unique obs: 5576 / CC1/2: 0.765

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.34→28.9 Å / SU ML: 0.2513 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.2129
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 446 5.15 %
Rwork0.2117 8219 -
obs0.2142 8665 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.43 Å2
Refinement stepCycle: LAST / Resolution: 2.34→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1126 0 48 29 1203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01241198
X-RAY DIFFRACTIONf_angle_d1.4231640
X-RAY DIFFRACTIONf_chiral_restr0.0632187
X-RAY DIFFRACTIONf_plane_restr0.0109207
X-RAY DIFFRACTIONf_dihedral_angle_d11.5234193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.670.27381110.22272359X-RAY DIFFRACTION81.73
2.67-3.370.29931600.23182896X-RAY DIFFRACTION99.54
3.37-28.90.23611750.19862964X-RAY DIFFRACTION96.88

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