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- PDB-6ifv: C-terminal truncated KsgA from Bacillus subtilis 168 -

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Basic information

Entry
Database: PDB / ID: 6ifv
TitleC-terminal truncated KsgA from Bacillus subtilis 168
ComponentsRibosomal RNA small subunit methyltransferase A
KeywordsTRANSFERASE / KsgA / resistance / Rossmann fold / truncation
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-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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.11 Å
AuthorsBhujbalrao, R. / Anand, R.
Funding support India, 1items
OrganizationGrant numberCountry
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)48,0962
Polymers48,0962
Non-polymers00
Water18010
1
A: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)24,0481
Polymers24,0481
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)24,0481
Polymers24,0481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.867, 77.867, 143.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 4 - 211 / Label seq-ID: 4 - 211

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 24048.135 Da / Num. of mol.: 2 / Fragment: C-terminal truncated
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.: 10 / 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: 2.27 Å3/Da / Density % sol: 45.86 % / Description: hexogonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES sodium pH 7.5, 1.4M Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→47.8 Å / Num. obs: 8452 / % possible obs: 99.8 % / Redundancy: 12.2 % / Rsym value: 0.178 / Net I/σ(I): 13.1
Reflection shellResolution: 3.11→3.11 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.727 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementResolution: 3.11→19.877 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.874 / SU B: 27.012 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.579 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1046 12.5 %RANDOM
Rwork0.18574 ---
obs0.19691 7311 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 3.11→19.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 0 10 3068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193105
X-RAY DIFFRACTIONr_bond_other_d0.0020.022992
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9824245
X-RAY DIFFRACTIONr_angle_other_deg0.99436890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8735406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30225.321109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01415506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.721511
X-RAY DIFFRACTIONr_chiral_restr0.0790.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213394
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
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_it3.7165.7491636
X-RAY DIFFRACTIONr_mcbond_other3.7175.7491635
X-RAY DIFFRACTIONr_mcangle_it5.9788.6132038
X-RAY DIFFRACTIONr_mcangle_other5.9778.6132039
X-RAY DIFFRACTIONr_scbond_it3.3155.9221468
X-RAY DIFFRACTIONr_scbond_other3.3135.9221469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4088.8122208
X-RAY DIFFRACTIONr_long_range_B_refined8.23668.5543188
X-RAY DIFFRACTIONr_long_range_B_other8.23168.5443188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11342 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.115→3.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 88 -
Rwork0.281 500 -
obs--98.99 %

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