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- PDB-7cs0: Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smeg... -

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Basic information

Entry
Database: PDB / ID: 7cs0
TitleAminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-Complex with Coenzyme A and Paromomycin
ComponentsAminoglycoside 2'-N-acetyltransferase
KeywordsTRANSFERASE / aminoglycoside acetyltransferase / antibiotics / paromomycin
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETATE ION / COENZYME A / PAROMOMYCIN / Aminoglycoside 2'-N-acetyltransferase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsJeong, C.S. / Hwang, J. / Do, H. / Lee, J.H.
CitationJournal: Sci Rep / Year: 2020
Title: Structural and biochemical analyses of an aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis.
Authors: Jeong, C.S. / Hwang, J. / Do, H. / Cha, S.S. / Oh, T.J. / Kim, H.J. / Park, H.H. / Lee, J.H.
History
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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)49,52913
Polymers46,3982
Non-polymers3,13211
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-30 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.374, 56.374, 122.866
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 23198.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: aac, MSMEG_0434, MSMEI_0423 / Production host: Escherichia coli (E. coli)
References: UniProt: P94968, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 6 types, 259 molecules

#2: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C23H45N5O14 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium acetate hydrate, 0.1M HEPES (pH 7.5), 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 27416 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 31.56
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.266 / Num. unique obs: 1389 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CRM

7crm


Resolution: 2.05→28.2 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.339 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.198 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23323 1413 5.2 %RANDOM
Rwork0.18306 ---
obs0.18564 25966 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.873 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.05→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 199 248 3359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133175
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172874
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6624333
X-RAY DIFFRACTIONr_angle_other_deg1.3121.5946609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5165370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71219.33194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38515462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9231540
X-RAY DIFFRACTIONr_chiral_restr0.0720.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
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_it2.1172.161493
X-RAY DIFFRACTIONr_mcbond_other2.1172.161492
X-RAY DIFFRACTIONr_mcangle_it3.3513.2211858
X-RAY DIFFRACTIONr_mcangle_other3.3513.2211859
X-RAY DIFFRACTIONr_scbond_it2.8062.6771682
X-RAY DIFFRACTIONr_scbond_other2.8052.6771683
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4823.9262476
X-RAY DIFFRACTIONr_long_range_B_refined6.79327.6823565
X-RAY DIFFRACTIONr_long_range_B_other6.74127.5343518
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 128 -
Rwork0.196 1884 -
obs--99.16 %

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