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- PDB-6vta: Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex ... -

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Basic information

Entry
Database: PDB / ID: 6vta
TitleAminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with amikacin and acetyl-CoA
ComponentsAminoglycoside 2'-N-acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase / GNAT superfamily
Function / homology
Function and homology information


gentamicin 2'-N-acetyltransferase / aminoglycoside 2'-N-acetyltransferase activity / response to antibiotic
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / Chem-AKN / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsBassenden, A.V. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-162365 Canada
CitationJournal: Sci Rep / Year: 2021
Title: Structural and phylogenetic analyses of resistance to next-generation aminoglycosides conferred by AAC(2') enzymes.
Authors: Bassenden, A.V. / Dumalo, L. / Park, J. / Blanchet, J. / Maiti, K. / Arya, D.P. / Berghuis, A.M.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside 2'-N-acetyltransferase
B: Aminoglycoside 2'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5726
Polymers40,7822
Non-polymers2,7904
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-20 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.367, 58.928, 83.203
Angle α, β, γ (deg.)90.00, 115.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-646-

HOH

31B-497-

HOH

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Components

#1: Protein Aminoglycoside 2'-N-acetyltransferase / AAC(2')-Ia


Mass: 20390.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Providencia stuartii (bacteria) / Gene: aac / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q52424, gentamicin 2'-N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKN / (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide / AMIKACIN


Mass: 585.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H43N5O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Na3Cit, NaCl, TRIS, amikacin, acetyl CoA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.42→27.47 Å / Num. obs: 76642 / % possible obs: 99.44 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 21.92
Reflection shellResolution: 1.42→1.471 Å / Mean I/σ(I) obs: 2.42 / Num. unique obs: 7629 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VR2

6vr2


Resolution: 1.42→27.47 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.56
RfactorNum. reflection% reflection
Rfree0.1823 3822 4.99 %
Rwork0.14 --
obs0.1421 76602 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.42→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 182 480 3491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053450
X-RAY DIFFRACTIONf_angle_d0.944730
X-RAY DIFFRACTIONf_dihedral_angle_d25.062494
X-RAY DIFFRACTIONf_chiral_restr0.075500
X-RAY DIFFRACTIONf_plane_restr0.003611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.430.35811420.31712494X-RAY DIFFRACTION93
1.43-1.450.31461700.28552632X-RAY DIFFRACTION98
1.45-1.470.31521450.25822645X-RAY DIFFRACTION98
1.47-1.490.32821370.24342681X-RAY DIFFRACTION99
1.49-1.520.30921600.22342643X-RAY DIFFRACTION99
1.52-1.540.26711480.20812673X-RAY DIFFRACTION99
1.54-1.570.2661310.19962686X-RAY DIFFRACTION99
1.57-1.590.22571120.18872696X-RAY DIFFRACTION99
1.59-1.620.24221470.17472704X-RAY DIFFRACTION99
1.62-1.650.21371460.15762655X-RAY DIFFRACTION100
1.65-1.690.22531430.14992701X-RAY DIFFRACTION100
1.69-1.720.21871490.14012699X-RAY DIFFRACTION100
1.72-1.760.18331350.12852690X-RAY DIFFRACTION100
1.76-1.810.18961400.12552700X-RAY DIFFRACTION100
1.81-1.860.19381450.12422686X-RAY DIFFRACTION100
1.86-1.910.16161490.12152714X-RAY DIFFRACTION100
1.91-1.970.16431270.11572726X-RAY DIFFRACTION100
1.97-2.040.18961340.11482730X-RAY DIFFRACTION100
2.04-2.120.13821580.11022691X-RAY DIFFRACTION100
2.12-2.220.15721160.11372724X-RAY DIFFRACTION100
2.22-2.340.1741360.12082707X-RAY DIFFRACTION100
2.34-2.480.15211290.12382725X-RAY DIFFRACTION100
2.48-2.680.17241410.13632753X-RAY DIFFRACTION100
2.68-2.950.16971660.14032699X-RAY DIFFRACTION100
2.95-3.370.15021510.12772730X-RAY DIFFRACTION100
3.37-4.240.12811320.10832785X-RAY DIFFRACTION100
4.25-27.470.14051330.12552811X-RAY DIFFRACTION100

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