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- PDB-6ifw: crystal structure of chimeric construct of KsgA with loop 1 from erm -

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Basic information

Entry
Database: PDB / ID: 6ifw
Titlecrystal structure of chimeric construct of KsgA with loop 1 from erm
ComponentsRibosomal RNA small subunit methyltransferase A
KeywordsTRANSFERASE / Chimera / erythromycin / resistance
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / RNA binding / cytosol
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 Å
AuthorsBhujbalrao, R. / Anand, R.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (India)SERB/F/4395/2016-17 India
Other government20150237B02RP00614-BRNS India
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Deciphering Determinants in Ribosomal Methyltransferases That Confer Antimicrobial Resistance.
Authors: Bhujbalrao, R. / Anand, R.
History
DepositionSep 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 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

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase A
B: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)61,4232
Polymers61,4232
Non-polymers00
Water19811
1
A: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)30,7111
Polymers30,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)30,7111
Polymers30,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.220, 81.000, 120.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase A / / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine ...16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine transferase / 16S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 30711.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rsmA, ksgA, BSU00420 / Production host: Escherichia coli (E. coli)
References: UniProt: P37468, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4% Tacsimate, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 15977 / % possible obs: 99.57 % / Redundancy: 10.2 % / Rsym value: 0.152 / Net I/σ(I): 27.76
Reflection shellResolution: 2.95→3.026 Å / Redundancy: 10 % / Mean I/σ(I) obs: 4.25 / Rsym value: 0.596 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementResolution: 2.95→38.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.891 / SU B: 21.065 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29418 775 6 %RANDOM
Rwork0.20059 ---
obs0.20622 12167 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.568 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.95→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 0 11 3794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193866
X-RAY DIFFRACTIONr_bond_other_d0.0020.023748
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9815249
X-RAY DIFFRACTIONr_angle_other_deg0.99238704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8245485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39525.904166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46515700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0161515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
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_it4.1956.351952
X-RAY DIFFRACTIONr_mcbond_other4.1946.3481951
X-RAY DIFFRACTIONr_mcangle_it6.6639.5082433
X-RAY DIFFRACTIONr_mcangle_other6.6639.5092434
X-RAY DIFFRACTIONr_scbond_it3.9266.8061914
X-RAY DIFFRACTIONr_scbond_other3.9196.8021912
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.47510.0682816
X-RAY DIFFRACTIONr_long_range_B_refined9.94276.1864023
X-RAY DIFFRACTIONr_long_range_B_other9.94176.1744023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 55 -
Rwork0.286 895 -
obs--100 %

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