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- PDB-3dmh: T. Thermophilus 16S rRNA N2 G1207 methyltransferase (RsmC) in com... -

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Basic information

Entry
Database: PDB / ID: 3dmh
TitleT. Thermophilus 16S rRNA N2 G1207 methyltransferase (RsmC) in complex with AdoMet and Guanosine
ComponentsProbable ribosomal RNA small subunit methyltransferase
KeywordsTRANSFERASE / monomethyltranserase / 16S rRNA methyltransferase / N2 G1207 methyltransferase / S-Adenosyl-L-Homocysteine / Translation / Methyltransferase
Function / homology
Function and homology information


rRNA (adenine-N6,N6-)-dimethyltransferase activity / nucleic acid binding / cytoplasm
Similarity search - Function
: / Methyltransferase small domain / Methyltransferase small domain / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...: / Methyltransferase small domain / Methyltransferase small domain / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE / S-ADENOSYLMETHIONINE / Probable ribosomal RNA small subunit methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsDemirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of the Thermus thermophilus 16 S rRNA Methyltransferase RsmC in Complex with Cofactor and Substrate Guanosine.
Authors: Demirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Probable ribosomal RNA small subunit methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4125
Polymers41,5381
Non-polymers8744
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.863, 86.234, 95.091
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 Probable ribosomal RNA small subunit methyltransferase


Mass: 41537.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cytoplasm / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0533 / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (Star)
References: UniProt: Q5SKW0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: microbatch technique under oil / pH: 8.5
Details: 0.085 M TRIS HCl (pH 8.5), 25.5% w/v PEG4000 15% 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 165 mm / Detector: CCD / Date: 2008
Details: Slits: Variable vertical and horizontal slits. Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. ...Details: Slits: Variable vertical and horizontal slits. Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m.
RadiationMonochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2. ...Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 57244 / % possible obs: 97.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 23.8
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3603 / % possible all: 81.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.679 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOR STRUCTURE DETERMINATION, AUTHORS STATE THAT THE INITIAL MODEL IS SOLVED BY USING ANOMALOUS DATA ON A CRYSTAL DIFFERENT FROM WHAT WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOR STRUCTURE DETERMINATION, AUTHORS STATE THAT THE INITIAL MODEL IS SOLVED BY USING ANOMALOUS DATA ON A CRYSTAL DIFFERENT FROM WHAT WAS DESCRIBED IN REMARK 200. THE FINAL STRUCTURE WAS REFINED BY USING THE INITIAL MODEL AND THE DATA DESCRIBED IN REMARK 3 AND REMARK 200.
RfactorNum. reflection% reflectionSelection details
Rfree0.22577 3060 5.1 %RANDOM
Rwork0.19355 ---
obs0.19518 57244 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.86 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 55 420 3308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222963
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3612.0114027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09922.24125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16715466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1751529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022260
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21443
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22022
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7071.51885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07822931
X-RAY DIFFRACTIONr_scbond_it1.89231216
X-RAY DIFFRACTIONr_scangle_it2.9764.51096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 200 -
Rwork0.303 3603 -
obs-3603 85 %
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)
10.8496-0.0706-0.61831.19630.54192.0769-0.06660.1336-0.09740.0587-0.00290.02970.3558-0.00120.0695-0.0403-0.00980.0053-0.0425-0.0131-0.053533.939250.0008-1.8573
21.95530.4829-0.01650.9861-0.10212.98030.0439-0.17210.04210.2696-0.03830.1007-0.0464-0.2093-0.0056-0.02250.01070.0447-0.08340.0082-0.06325.319161.124325.2918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1783 - 178
2X-RAY DIFFRACTION2AA187 - 372187 - 372

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