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- PDB-6vr2: Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex ... -

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Basic information

Entry
Database: PDB / ID: 6vr2
TitleAminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with acetylated-tobramycin 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
ACETATE ION / COENZYME A / Chem-R7Y / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 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)43,18513
Polymers40,2172
Non-polymers2,96711
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-18 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.798, 72.798, 146.321
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: 20108.693 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-R7Y / (1S,2S,3R,4S,6R)-3-{[2-(acetylamino)-6-amino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl]oxy}-4,6-diamino-2-hydroxycycloh exyl 3-amino-3-deoxy-alpha-D-glucopyranoside / acetylated-tobramycin


Mass: 509.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H39N5O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: MPD, sodium acetate, tobramycin, 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: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.77→26.47 Å / Num. obs: 44518 / % possible obs: 99.89 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 22.65
Reflection shellResolution: 1.77→1.833 Å / Mean I/σ(I) obs: 2.52 / Num. unique obs: 4369 / CC1/2: 0.654 / CC star: 0.889

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Processing

Software
NameVersionClassification
PHENIX(1.17_3644: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JZS

7jzs


Resolution: 1.77→26.47 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.41
RfactorNum. reflection% reflection
Rfree0.1924 3767 4.46 %
Rwork0.1671 --
obs0.1682 84556 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.77→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 194 324 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063176
X-RAY DIFFRACTIONf_angle_d0.9054314
X-RAY DIFFRACTIONf_dihedral_angle_d30.0831147
X-RAY DIFFRACTIONf_chiral_restr0.052456
X-RAY DIFFRACTIONf_plane_restr0.004547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.31741290.32482593X-RAY DIFFRACTION87
1.79-1.810.3051360.31022994X-RAY DIFFRACTION99
1.81-1.840.25311420.27713009X-RAY DIFFRACTION100
1.84-1.860.25471340.24263009X-RAY DIFFRACTION100
1.86-1.890.27971360.22772985X-RAY DIFFRACTION100
1.89-1.920.26061340.20623059X-RAY DIFFRACTION100
1.92-1.950.22931420.20542995X-RAY DIFFRACTION100
1.95-1.990.24281480.19272983X-RAY DIFFRACTION100
1.99-2.020.21941480.18533040X-RAY DIFFRACTION100
2.02-2.060.22671320.18372956X-RAY DIFFRACTION100
2.06-2.10.19631460.18153049X-RAY DIFFRACTION100
2.1-2.150.21041360.16793017X-RAY DIFFRACTION100
2.15-2.20.22251440.17112999X-RAY DIFFRACTION100
2.2-2.250.16491440.16532964X-RAY DIFFRACTION100
2.25-2.310.1911440.16163012X-RAY DIFFRACTION100
2.31-2.380.23531320.16313022X-RAY DIFFRACTION100
2.38-2.460.20291410.16882999X-RAY DIFFRACTION100
2.46-2.550.18151320.16813047X-RAY DIFFRACTION100
2.55-2.650.19471440.16332982X-RAY DIFFRACTION100
2.65-2.770.18291460.16683000X-RAY DIFFRACTION100
2.77-2.920.18941460.15963058X-RAY DIFFRACTION100
2.92-3.10.16521390.15792973X-RAY DIFFRACTION100
3.1-3.340.21021400.153019X-RAY DIFFRACTION100
3.34-3.670.16881380.14122984X-RAY DIFFRACTION100
3.67-4.20.16171500.1313010X-RAY DIFFRACTION100
4.2-5.280.11711360.12663008X-RAY DIFFRACTION100
5.29-26.540.18491280.16353023X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.8903 Å / Origin y: 30.501 Å / Origin z: 18.9672 Å
111213212223313233
T0.1124 Å20.0006 Å2-0.0054 Å2-0.1003 Å20.0082 Å2--0.0928 Å2
L1.1192 °20.1619 °2-0.0721 °2-1.5537 °2-0.0342 °2--0.6449 °2
S0.0495 Å °-0.0207 Å °0.0101 Å °0.1304 Å °-0.0239 Å °-0.0082 Å °0.0111 Å °-0.0175 Å °-0.0187 Å °
Refinement TLS groupSelection details: all

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