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- PDB-3fuw: T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA)... -

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Basic information

Entry
Database: PDB / ID: 3fuw
TitleT. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with 5'-methylthioadenosine in space group P212121
ComponentsDimethyladenosine transferase
KeywordsTRANSFERASE / Methyltransferase / dimethyltransferase / dual-specific methyltransferase / 16S rRNA methyltransferase / translation / Antibiotic resistance / RNA-binding / rRNA processing / S-adenosyl-L-methionine
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 / RNA binding / cytoplasm
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
5'-DEOXY-5'-METHYLTHIOADENOSINE / Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.56 Å
AuthorsDemirci, H. / Belardinelli, R. / Seri, E. / Gregory, S.T. / Gualerzi, C. / Dahlberg, A.E. / Jogl, G.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.
Authors: Demirci, H. / Belardinelli, R. / Seri, E. / Gregory, S.T. / Gualerzi, C. / Dahlberg, A.E. / Jogl, G.
History
DepositionJan 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dimethyladenosine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2062
Polymers29,9091
Non-polymers2971
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.417, 61.042, 82.531
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dimethyladenosine transferase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase / 16S rRNA dimethylase / High ...S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase / 16S rRNA dimethylase / High level kasugamycin resistance protein ksgA / Kasugamycin dimethyltransferase


Mass: 29908.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cytoplasm / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: ksgA, TTHA0083 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)Star
References: UniProt: Q5SM60, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 277 K / Method: microbatch technique under oil / pH: 8.5
Details: 17% w/v polyethylene glycol 4000, 85 mM HEPES-NaOH (pH 8.5), 8.5% v/v isopropanol and 15% v/v anhydrous glycerol, microbatch technique under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9797 Å
DetectorType: MAR CCD 130 mm / Detector: CCD
Details: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror
RadiationMonochromator: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.56→30 Å / Num. obs: 38372 / % possible obs: 97 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.67
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.64 / Num. unique all: 3682 / % possible all: 94.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.56→28.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.08 / SU B: 3.348 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1905 5 %RANDOM
Rwork0.197 ---
obs0.199 37953 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.79 Å2 / Biso mean: 19.766 Å2 / Biso min: 4.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.56→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 20 335 2416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222148
X-RAY DIFFRACTIONr_angle_refined_deg1.3412.0122926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.1112190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9515352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1621528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221631
X-RAY DIFFRACTIONr_mcbond_it0.591.51330
X-RAY DIFFRACTIONr_mcangle_it1.02522142
X-RAY DIFFRACTIONr_scbond_it1.8893818
X-RAY DIFFRACTIONr_scangle_it3.0794.5784
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 139 -
Rwork0.227 2524 -
all-2663 -
obs-2524 94.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.09660.4334-0.5831.8327-0.50721.0001-0.0194-0.0453-0.0992-0.2022-0.0534-0.26180.0790.07070.07270.0302-0.00310.03170.0468-0.00160.04432.0037-15.8694-15.27
21.3774-0.1508-0.66681.2462-0.34310.64590.1070.00250.0904-0.0318-0.01960.0146-0.0981-0.011-0.08740.0404-0.02160.02120.0461-0.00410.014320.7388-9.5532-11.4421
31.6645-1.2442-0.57532.75810.1861.08270.2659-0.10340.2655-0.1181-0.05-0.0024-0.267-0.0561-0.21580.08650.00310.09290.0906-0.00440.13520.34198.0529-4.6169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 80
2X-RAY DIFFRACTION2A81 - 200
3X-RAY DIFFRACTION3A201 - 271

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