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- PDB-6vr3: Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex ... -

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Basic information

Entry
Database: PDB / ID: 6vr3
TitleAminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with acetylated-netilmicin and 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
COENZYME A / Chem-NTL / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 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 6, 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)43,0646
Polymers40,4942
Non-polymers2,5704
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.038, 73.038, 145.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 20246.842 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-NTL / N-[(2S,3R)-2-{[(1R,2S,3S,4R,6S)-6-amino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-lyxopyranosyl]oxy}-4-(ethylamino) -2-hydroxycyclohexyl]oxy}-6-(aminomethyl)-3,4-dihydro-2H-pyran-3-yl]acetamide / acetylated-netilmicin


Mass: 517.616 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H43N5O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: NaSCN, MPD, Acetyl CoA, Netilmicin

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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: Feb 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2→26.49 Å / Num. obs: 58685 / % possible obs: 99.92 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 20.82
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 3059 / CC1/2: 0.761 / CC star: 0.913

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Processing

Software
NameVersionClassification
PHENIX(1.17_3644: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6VR2

6vr2


Resolution: 2→26.49 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.14
RfactorNum. reflection% reflection
Rfree0.226 3770 6.42 %
Rwork0.1805 --
obs0.1834 58685 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 168 170 3084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083050
X-RAY DIFFRACTIONf_angle_d0.8664147
X-RAY DIFFRACTIONf_dihedral_angle_d31.3381061
X-RAY DIFFRACTIONf_chiral_restr0.052441
X-RAY DIFFRACTIONf_plane_restr0.004515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.35191480.31662061X-RAY DIFFRACTION100
2.03-2.050.34291280.29862005X-RAY DIFFRACTION99
2.05-2.080.31451460.27272047X-RAY DIFFRACTION100
2.08-2.110.30531350.26342006X-RAY DIFFRACTION100
2.11-2.140.30011440.24452089X-RAY DIFFRACTION100
2.14-2.170.26151440.23762016X-RAY DIFFRACTION100
2.17-2.210.29481380.22342026X-RAY DIFFRACTION100
2.21-2.250.26271380.22381998X-RAY DIFFRACTION100
2.25-2.290.30951460.21642075X-RAY DIFFRACTION100
2.29-2.330.24681300.20522013X-RAY DIFFRACTION100
2.33-2.380.23631410.19832032X-RAY DIFFRACTION100
2.38-2.430.26691420.18632069X-RAY DIFFRACTION100
2.43-2.490.29021420.20841971X-RAY DIFFRACTION100
2.49-2.550.24941380.19922063X-RAY DIFFRACTION100
2.55-2.620.25541380.18982007X-RAY DIFFRACTION100
2.62-2.70.25851380.19632064X-RAY DIFFRACTION100
2.7-2.780.29261400.19522045X-RAY DIFFRACTION100
2.78-2.880.24771240.18032034X-RAY DIFFRACTION100
2.88-30.21641400.17122010X-RAY DIFFRACTION100
3-3.140.19181380.16932038X-RAY DIFFRACTION100
3.14-3.30.17991420.16062052X-RAY DIFFRACTION100
3.3-3.510.19021380.15432056X-RAY DIFFRACTION100
3.51-3.780.18381460.14411991X-RAY DIFFRACTION100
3.78-4.150.18321410.13472027X-RAY DIFFRACTION100
4.16-4.750.1591400.12812031X-RAY DIFFRACTION100
4.75-5.980.16671450.16332050X-RAY DIFFRACTION100
5.98-26.490.25111400.17822039X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 59.3731 Å / Origin y: 30.4961 Å / Origin z: 164.8221 Å
111213212223313233
T0.1446 Å2-0.0088 Å20.0004 Å2-0.1465 Å20.0118 Å2--0.1243 Å2
L1.7161 °2-0.1581 °2-0.0638 °2-2.0935 °2-0.0451 °2--0.7549 °2
S0.084 Å °0.0345 Å °0.064 Å °0.1214 Å °-0.0686 Å °-0.0629 Å °-0.0133 Å °-0.0495 Å °-0.0129 Å °
Refinement TLS groupSelection details: all

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