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- PDB-7jzs: Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex ... -

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Basic information

Entry
Database: PDB / ID: 7jzs
TitleAminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with 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 / DI(HYDROXYETHYL)ETHER / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPark, J. / Bassenden, 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
DepositionSep 2, 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 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7005
Polymers20,6341
Non-polymers1,0664
Water3,423190
1
A: Aminoglycoside 2'-N-acetyltransferase
hetero molecules

A: Aminoglycoside 2'-N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,40010
Polymers41,2682
Non-polymers2,1328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2290 Å2
ΔGint-14 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.720, 58.720, 120.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-466-

HOH

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Components

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


Mass: 20634.213 Da / Num. of mol.: 1
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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: ammonium sulfate, PEG 400, HEPES

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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: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.3→52.75 Å / Num. obs: 52444 / % possible obs: 99.95 % / Redundancy: 12.1 % / CC1/2: 1 / Net I/σ(I): 28.09
Reflection shellResolution: 1.3→1.346 Å / Mean I/σ(I) obs: 2.55 / Num. unique obs: 5117 / CC1/2: 0.646

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5US1

5us1


Resolution: 1.3→52.75 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.521 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18425 2675 5.1 %RANDOM
Rwork0.13809 ---
obs0.14039 49768 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.3→52.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 65 190 1689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0191850
X-RAY DIFFRACTIONr_bond_other_d0.0030.021588
X-RAY DIFFRACTIONr_angle_refined_deg2.5281.9622539
X-RAY DIFFRACTIONr_angle_other_deg1.22233711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00724.71989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.666158
X-RAY DIFFRACTIONr_chiral_restr0.1570.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022193
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3162.518899
X-RAY DIFFRACTIONr_mcbond_other4.3012.516898
X-RAY DIFFRACTIONr_mcangle_it4.973.7781164
X-RAY DIFFRACTIONr_mcangle_other4.9683.7791165
X-RAY DIFFRACTIONr_scbond_it6.8522.943951
X-RAY DIFFRACTIONr_scbond_other6.8522.942951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8824.291376
X-RAY DIFFRACTIONr_long_range_B_refined7.3229.9051993
X-RAY DIFFRACTIONr_long_range_B_other7.3229.91993
X-RAY DIFFRACTIONr_rigid_bond_restr6.2533438
X-RAY DIFFRACTIONr_sphericity_free31.3175101
X-RAY DIFFRACTIONr_sphericity_bonded17.21553469
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 192 -
Rwork0.213 3603 -
obs--99.87 %

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