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Yorodumi- PDB-2v3k: The yeast ribosome synthesis factor Emg1 alpha beta knot fold met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v3k | ||||||
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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 / rRNA (pseudouridine) methyltransferase activity / nuclear microtubule / 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 / 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 ...rRNA small subunit pseudouridine methyltransferase Nep1 / rRNA (pseudouridine) methyltransferase activity / nuclear microtubule / 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 / 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 / 90S preribosome / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Leulliot, N. / Bohnsack, M.T. / Graille, M. / Tollervey, D. / VanTilbeurgh, 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 | 2v3k.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v3k.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v3k_validation.pdf.gz | 777.1 KB | Display | wwPDB validaton report |
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Full document | 2v3k_full_validation.pdf.gz | 778.7 KB | Display | |
Data in XML | 2v3k_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 2v3k_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/2v3k ftp://data.pdbj.org/pub/pdb/validation_reports/v3/2v3k | HTTPS FTP |
-Related structure data
Related structure data | 2v3jSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: Chemical | ChemComp-SAM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.74 % |
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Crystal grow | pH: 7.5 Details: 25% PEG4K, 0.2M LI2SO4, 0.1M TRIS PH7.5, 20% GLYCEROL, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.2 Å / Num. obs: 20687 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V3J Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 3.514 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.157 / 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: 27.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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