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- PDB-3mti: The Crystal Structure of a rRNA Methylase from Streptococcus ther... -

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Basic information

Entry
Database: PDB / ID: 3mti
TitleThe Crystal Structure of a rRNA Methylase from Streptococcus thermophilus to 1.95A
ComponentsrRNA methylase
KeywordsTRANSFERASE / SAM-dependent / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Putative rRNA methylase / Putative rRNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
rRNA methylase (SAM-dependent methyltransferase superfamily), putative
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsStein, A.J. / Mulligan, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of a rRNA Methylase from Streptococcus thermophilus to 1.95A
Authors: Stein, A.J. / Mulligan, R. / Freeman, L. / Joachimiak, A.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rRNA methylase
B: rRNA methylase


Theoretical massNumber of molelcules
Total (without water)41,9922
Polymers41,9922
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.331, 57.044, 75.365
Angle α, β, γ (deg.)90.000, 109.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein rRNA methylase / SAM-dependent methyltransferase superfamily


Mass: 20995.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Strain: LMG 18311 / Gene: stu1645 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5M2Z6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.1M HEPES pH 7.5, 0.2M Sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 28265 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.085 / Χ2: 1.874 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.023.20.57828360.50499.9
2.02-2.13.20.40928340.56599.9
2.1-2.23.20.32628190.62799.9
2.2-2.313.30.27827841.04999.9
2.31-2.463.30.18428150.793100
2.46-2.653.30.13528380.946100
2.65-2.913.30.09628471.357100
2.91-3.333.30.07328362.074100
3.33-4.23.20.05728153.2398.5
4.2-503.20.06628417.75196.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.326 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1421 5 %RANDOM
Rwork0.238 ---
obs0.24 28165 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-2.44 Å2
2---4.43 Å20 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 0 125 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222708
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9833672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94724.959123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94615462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5731515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212027
X-RAY DIFFRACTIONr_mcbond_it0.6681.51718
X-RAY DIFFRACTIONr_mcangle_it1.22122749
X-RAY DIFFRACTIONr_scbond_it2.1973990
X-RAY DIFFRACTIONr_scangle_it3.2394.5922
LS refinement shellResolution: 1.949→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 112 -
Rwork0.387 1865 -
all-1977 -
obs--95 %

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