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- PDB-2zwv: Crystal structure of Thermus thermophilus 16S rRNA methyltransfer... -

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Basic information

Entry
Database: PDB / ID: 2zwv
TitleCrystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533)
ComponentsProbable ribosomal RNA small subunit methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / 16S RRNA METHYLTRANSFERASE / S-ADENOSYL-L-HOMOCYSTEINE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, H. / Kawazoe, M. / Kaminishi, T. / Tatsuguchi, A. / Naoe, C. / Terada, T. / Shirouzu, M. / Takemoto, C. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533)
Authors: Wang, H. / Kawazoe, M. / Kaminishi, T. / Tatsuguchi, A. / Naoe, C. / Terada, T. / Shirouzu, M. / Takemoto, C. / Yokoyama, S.
History
DepositionDec 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)41,0932
Polymers40,7091
Non-polymers3841
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)50.178, 80.093, 93.689
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 / 16S rRNA methyltransferase RsmC / TTHA0533


Mass: 40708.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0533 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKW0
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 0.4M Potassium sodium tartrate, 0.25% Polyethylene glycol MME 5000, 0.05M TRIS pH8.5, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 26313 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 3.9 Å2 / Rsym value: 0.14 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2555 / Rsym value: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZUL
Resolution: 2→38.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 58745.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2459 9.8 %RANDOM
Rwork0.189 ---
obs0.189 25137 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6129 Å2 / ksol: 0.378591 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20 Å2
2---1.23 Å20 Å2
3----1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 26 238 3120
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 372 9.5 %
Rwork0.196 3535 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4sah_xplor_par.txt

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