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Yorodumi- PDB-1yn2: Solution structure of the Neurospora VS ribozyme stem-loop V in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yn2 | ||||||
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Title | Solution structure of the Neurospora VS ribozyme stem-loop V in the presence of MgCl2 with modeling of bound manganese ions | ||||||
Components | VS RIBOZYME STEM-LOOP V | ||||||
Keywords | RNA / U-turn / hairpin / magnesium ions / manganese ions / paramagnetic | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS | ||||||
Model type details | minimized average | ||||||
Authors | Campbell, D.O. / Legault, P. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: NMR structure of varkud satellite ribozyme stem-loop v in the presence of magnesium ions and localization of metal-binding sites Authors: Campbell, D.O. / Bouchard, P. / Desjardins, G. / Legault, P. #1: Journal: To be Published / Year: 2005 Title: NMR Structure of the VS Ribozyme Stem-Loop V RNA and Magnesium-Ion Binding from Chemical-Shift Mapping Authors: Campbell, D.O. / Legault, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yn2.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yn2.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1yn2 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1yn2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 5419.261 Da / Num. of mol.: 1 / Fragment: SL5 / Source method: obtained synthetically Details: THIS SEQUENCE IS DERIVED FROM THE NEUROSPORA VARKUD SATELLITE RIBOZYME | ||
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#2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Bound manganese ions were modeled using distance restraints derived from Mn-induced paramagnetic line broadening |
-Sample preparation
Details | Contents: 0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5 Solvent system: [10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 ...Solvent system: [10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added. |
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Sample conditions | Ionic strength: variable (see sample details) / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1 Details: Conformer 1 represents the minimized average structure, the 10 following structures represent the ensemble of low-energy structures | ||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 46 / Conformers submitted total number: 11 |