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- PDB-1yn1: Solution structure of the VS ribozyme stem-loop V in the presence... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yn1 | ||||||
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Title | Solution structure of the VS ribozyme stem-loop V in the presence of MgCl2 | ||||||
![]() | VS RIBOZYME STEM-LOOP V | ||||||
![]() | RNA / U-turn / hairpin / magnesium ions | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING; MOLECULAR DYNAMICS | ||||||
Model type details | minimized average | ||||||
![]() | Campbell, D.O. / Legault, P. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.2 KB | Display | ![]() |
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PDB format | ![]() | 100.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 324 KB | Display | ![]() |
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Full document | ![]() | 384.7 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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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 MgCl2]; 90% H2O, 10% D2O or 100% D2O; |
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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: 69 / Conformers submitted total number: 11 |