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

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Basic information

Entry
Database: PDB / ID: 3dmg
TitleT. Thermophilus 16S rRNA N2 G1207 methyltransferase (RsmC) in complex with AdoHcy
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 / tRNA processing / nucleic acid binding
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
S-ADENOSYL-L-HOMOCYSTEINE / 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)42,4998
Polymers41,5381
Non-polymers9617
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.968, 87.995, 94.930
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: microbatch technique under oil / pH: 7.5
Details: 0.1 M HEPES (pH 7.5) 1.5 M lithium sulfate monohydrate, 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: 58855 / % possible obs: 99.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.7
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4186 / % possible all: 96.5

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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: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.607 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.084 / 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 THEY SOLVED THESE STRUCTURES BY USING AN ANOMALOUS DATA FROM ANOTHER CRYSTAL. AUTHORS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOR STRUCTURE DETERMINATION, AUTHORS STATE THAT THEY SOLVED THESE STRUCTURES BY USING AN ANOMALOUS DATA FROM ANOTHER CRYSTAL. AUTHORS REFINED THESE DATASETS BY USING PREVIOUS MODEL WITHOUT ANY MOLECULAR REPLACEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.22032 3143 5.1 %RANDOM
Rwork0.18424 ---
obs0.18607 58855 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 56 716 3605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222986
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3042.0074063
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7922.222126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06115470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1011530
X-RAY DIFFRACTIONr_chiral_restr0.0810.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022281
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21458
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22055
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2373
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6641.51907
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03922969
X-RAY DIFFRACTIONr_scbond_it1.86131201
X-RAY DIFFRACTIONr_scangle_it2.8564.51094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 233 -
Rwork0.266 4186 -
obs-4186 97.29 %
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)
11.0928-0.0143-0.36221.45880.43751.4019-0.01690.2494-0.14010.0203-0.01060.03210.25890.01350.0275-0.0497-0.0105-0.00860.0003-0.0329-0.067134.151.286-2
21.78390.1739-0.07321.0772-0.40942.6537-0.0256-0.1565-0.01080.33330.00660.1095-0.1416-0.18020.0190.00620.01740.044-0.06510.0181-0.075425.46561.91625.277
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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