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Yorodumi- PDB-2v3j: The yeast ribosome synthesis factor Emg1 alpha beta knot fold met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v3j | ||||||
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Title | The yeast ribosome synthesis factor Emg1 alpha beta knot fold methyltransferase | ||||||
Components | ESSENTIAL FOR MITOTIC GROWTH 1 | ||||||
Keywords | RIBOSOMAL PROTEIN / EMG1 / RRNA PROCESSING / NUCLEAR PROTEIN / RIBONUCLEOPROTEIN / RIBOSOME BIOGENESIS / ALPHA/BETA KNOT FOLD METHYLTRANSFERASE | ||||||
Function / homology | Function and homology information rRNA small subunit pseudouridine methyltransferase Nep1 / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA base methylation / rRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...rRNA small subunit pseudouridine methyltransferase Nep1 / nuclear microtubule / rRNA (pseudouridine) methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA base methylation / rRNA methylation / Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / rRNA binding / nucleolus / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Leulliot, N. / Bohnsack, M.T. / Graille, M. / Tollervey, D. / Van Tilbeurgh, H. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2008 Title: The Yeast Ribosome Synthesis Factor Emg1 is a Novel Member of the Superfamily of Alpha/Beta Knot Fold Methyltransferases. Authors: Leulliot, N. / Bohnsack, M.T. / Graille, M. / Tollervey, D. / Van Tilbeurgh, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v3j.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v3j.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 2v3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v3j_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 2v3j_full_validation.pdf.gz | 423.3 KB | Display | |
Data in XML | 2v3j_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 2v3j_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/2v3j ftp://data.pdbj.org/pub/pdb/validation_reports/v3/2v3j | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29046.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q06287 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.72 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 25% PEG4K, 0.2M LI2SO4, 0.1M TRIS PH7.5, 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97953 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97953 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→19 Å / Num. obs: 20207 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.94→2.05 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4 / % possible all: 61.1 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2→19.01 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.075 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.01 Å
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