+Open data
-Basic information
Entry | Database: PDB / ID: 1t4o | ||||||
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Title | Crystal structure of rnt1p dsRBD | ||||||
Components | Ribonuclease III | ||||||
Keywords | HYDROLASE / Rnt1p / dsRBD / RNA-binding | ||||||
Function / homology | Function and homology information box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / ribonuclease III activity / termination of RNA polymerase II transcription ...box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / ribonuclease III activity / termination of RNA polymerase II transcription / rRNA transcription / rRNA processing / double-stranded RNA binding / chromatin organization / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Leulliot, N. / Quevillon-Cheruel, S. / Graille, M. / van Tilbeurgh, H. / Leeper, T.C. / Godin, K.S. / Edwards, T.E. / Sigurdsson, S.T. / Rozenkrants, N. / Nagel, R.J. ...Leulliot, N. / Quevillon-Cheruel, S. / Graille, M. / van Tilbeurgh, H. / Leeper, T.C. / Godin, K.S. / Edwards, T.E. / Sigurdsson, S.T. / Rozenkrants, N. / Nagel, R.J. / Ares Jr., M. / Varani, G. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III Authors: Leulliot, N. / Quevillon-Cheruel, S. / Graille, M. / Van Tilbeurgh, H. / Leeper, T.C. / Godin, K.S. / Edwards, T.E. / Sigurdsson, S.T. / Rozenkrants, N. / Nagel, R.J. / Ares, M. / Varani, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t4o.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t4o.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 1t4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/1t4o ftp://data.pdbj.org/pub/pdb/validation_reports/t4/1t4o | HTTPS FTP |
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-Related structure data
Related structure data | 1t4nSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13207.278 Da / Num. of mol.: 2 / Fragment: dsRBD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RNT1, YMR239C, YM9408.01C, YM9959.21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02555, ribonuclease III #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / pH: 8.5 Details: 0.2M lithium sulfate, 30% PEG 4000, 12% MPD, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2003 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.8 Å / Num. obs: 7943 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.56 Å / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T4N Resolution: 2.5→48.8 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.581 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.311 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.195 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20 /
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