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- PDB-2pjd: Crystal structure of 16S rRNA methyltransferase RsmC -

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Basic information

Entry
Database: PDB / ID: 2pjd
TitleCrystal structure of 16S rRNA methyltransferase RsmC
ComponentsRibosomal RNA small subunit methyltransferase C
KeywordsTRANSFERASE / gene duplication / RNA modification / SAM binding
Function / homology
Function and homology information


16S rRNA (guanine1207-N2)-methyltransferase / 16S rRNA (guanine(1207)-N(2))-methyltransferase activity / rRNA (guanine-N2-)-methyltransferase activity / rRNA base methylation / rRNA methylation / nucleic acid binding / cytoplasm / cytosol
Similarity search - Function
Methyltransferase small, N-terminal / rRNA small subunit methyltransferase C / Methyltransferase small domain N-terminal / Methyltransferase small domain / Methyltransferase small domain / 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
Ribosomal RNA small subunit methyltransferase C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSunita, S. / Purta, E. / Durawa, M. / Tkaczuk, K.L. / Bujnicki, J.M. / Sivaraman, J.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC
Authors: Sunita, S. / Purta, E. / Durawa, M. / Tkaczuk, K.L. / Swaathi, J. / Bujnicki, J.M. / Sivaraman, J.
History
DepositionApr 16, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase C


Theoretical massNumber of molelcules
Total (without water)37,9031
Polymers37,9031
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.939, 51.503, 73.330
Angle α, β, γ (deg.)90.00, 121.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase C / rRNA (guanine-N(2)-)-methyltransferase / 16S rRNA m2G1207 methyltransferase / RsmC protein


Mass: 37903.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rsmC / Plasmid: pCA24N / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P39406, EC: 2.1.1.52
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG MME 5000, 0.1M Tris-HCl pH8.5, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 25390 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.081 / Rsym value: 0.079 / Net I/σ(I): 12.9
Reflection shellResolution: 2.04→2.11 Å / Mean I/σ(I) obs: 15.2 / Rsym value: 0.074 / % possible all: 93.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
SHARPphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→15 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3223 -random
Rwork0.204 ---
obs0.256 23420 93.5 %-
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 0 232 2719

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