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

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Basic information

Entry
Database: PDB / ID: 6vou
TitleAminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with acetylated-plazomicin 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-PZC / 3,3',3''-phosphanetriyltripropanoic acid / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsBassenden, A.V. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-162365 Canada
CitationJournal: Commun Biol / Year: 2021
Title: Structural basis for plazomicin antibiotic action and resistance.
Authors: Golkar, T. / Bassenden, A.V. / Maiti, K. / Arya, D.P. / Schmeing, T.M. / Berghuis, A.M.
History
DepositionJan 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)43,90310
Polymers40,4942
Non-polymers3,4098
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-33 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.510, 73.510, 147.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 124 molecules

#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PZC / (2S)-N-[(1R,2S,3S,4R,5S)-4-{[(2S,3R)-3-(acetylamino)-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-yl]oxy}-5-amino-2-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]-4-amino-2-hydroxybutanamide / acetylated-plazomicin


Mass: 634.719 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H50N6O11 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: acetyl CoA, plazomicin, LiCl, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.95→63.66 Å / Num. obs: 33925 / % possible obs: 98.76 % / Redundancy: 8.1 % / Biso Wilson estimate: 39.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05153 / Rpim(I) all: 0.0185 / Rrim(I) all: 0.05489 / Net I/σ(I): 18.89
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 3293 / CC1/2: 0.718 / CC star: 0.914

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→63.66 Å / SU ML: 0.2178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 2001 5.9 %
Rwork0.1916 31921 -
obs0.1935 33922 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→63.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 224 116 3078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623043
X-RAY DIFFRACTIONf_angle_d0.9484125
X-RAY DIFFRACTIONf_chiral_restr0.0548440
X-RAY DIFFRACTIONf_plane_restr0.0041501
X-RAY DIFFRACTIONf_dihedral_angle_d32.01931086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.34151400.2812225X-RAY DIFFRACTION97.53
2-2.050.32731370.2562218X-RAY DIFFRACTION97.39
2.05-2.110.27961370.24612205X-RAY DIFFRACTION97.46
2.11-2.180.26881420.2212223X-RAY DIFFRACTION98.05
2.18-2.260.27011410.21622223X-RAY DIFFRACTION97.69
2.26-2.350.26791420.21072243X-RAY DIFFRACTION98.47
2.35-2.460.22441450.19692277X-RAY DIFFRACTION98.9
2.46-2.590.2451410.22462267X-RAY DIFFRACTION99.59
2.59-2.750.24821430.2162268X-RAY DIFFRACTION99.3
2.75-2.960.23111480.2172316X-RAY DIFFRACTION99.48
2.96-3.260.23481410.19792291X-RAY DIFFRACTION99.71
3.26-3.730.24481480.18452330X-RAY DIFFRACTION99.64
3.73-4.70.17351420.15682357X-RAY DIFFRACTION99.64
4.7-63.660.20131540.17872478X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: -33.7750626502 Å / Origin y: 3.47799312622 Å / Origin z: -5.41677215527 Å
111213212223313233
T0.294683938983 Å2-0.0351344183329 Å2-0.00633853113893 Å2-0.260091474102 Å20.0078577502948 Å2--0.259027852886 Å2
L1.86151669155 °2-0.132968155029 °2-0.162772093777 °2-1.74539504486 °2-0.0137567705095 °2--0.725640306347 °2
S-0.108631755376 Å °0.0118049010471 Å °0.104298519791 Å °0.0824331739856 Å °0.101305300129 Å °0.0429155530011 Å °0.0610893468488 Å °-0.0179783119112 Å °0.00702228969359 Å °
Refinement TLS groupSelection details: all

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