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

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Basic information

Entry
Database: PDB / ID: 3fuu
TitleT. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with Adenosine 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
ADENOSINE / Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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
A: ADENOSINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1762
Polymers29,9091
Non-polymers2671
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.195, 61.263, 82.719
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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 45.41 %
Crystal growTemperature: 277 K / Method: microbatch technique under oil / pH: 7.5
Details: 50 mM magnesium chloride hexahydrate, 100 mM HEPES (pH 7.5) and 30% v/v polyethylene glycol monomethyl ether 550, 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: 1.53→25 Å / Num. obs: 41095 / % possible obs: 98.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.27
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4080 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.53→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.127 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2054 5.1 %RANDOM
Rwork0.213 ---
obs0.215 40638 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.07 Å2 / Biso mean: 25.428 Å2 / Biso min: 14.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.25 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.53→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 19 378 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222171
X-RAY DIFFRACTIONr_angle_refined_deg1.4142.0112960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.76821.08792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52915356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9951528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021658
X-RAY DIFFRACTIONr_nbd_refined0.2020.21050
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.241
X-RAY DIFFRACTIONr_mcbond_it0.7231.51375
X-RAY DIFFRACTIONr_mcangle_it1.07522163
X-RAY DIFFRACTIONr_scbond_it1.9353884
X-RAY DIFFRACTIONr_scangle_it2.9074.5797
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 144 -
Rwork0.287 2861 -
all-3005 -
obs-2861 99.64 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0502-0.47710.86931.3779-0.64171.1074-0.0926-0.00140.14540.19050.0304-0.1888-0.0777-0.01860.0622-0.02640.013-0.038-0.0231-0.0248-0.02432.003516.18815.1048
21.27490.16920.70560.7722-0.13430.54490.0268-0.047-0.06090.06670.03130.02390.0274-0.0393-0.0581-0.02940.0309-0.0078-0.0139-0.0025-0.04120.9799.7511.4304
31.95791.31861.28442.73120.54021.80570.41310.047-0.24590.07580.02060.06220.3499-0.1342-0.4337-0.0102-0.0142-0.1205-0.0390.02850.04230.4136-7.98834.6707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 80
2X-RAY DIFFRACTION2A81 - 200
3X-RAY DIFFRACTION3A201 - 268

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