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Yorodumi- PDB-2rpk: Solution Structure of Domain II of the Positive Polarity CCHMVD H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rpk | ||||||||||||||||||||
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Title | Solution Structure of Domain II of the Positive Polarity CCHMVD Hammerhead Ribozyme | ||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / HAMMERHEAD RIBOZYME / VIROID / CCHMVD / HEXALOOP | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, restrained energy minimization | Model type details | minimized average | Authors | Gallego, J. / Dufour, D. / de la Pena, M. / Gago, S. / Flores, R. | Citation | Journal: Nucleic Acids Res. / Year: 2009 | Title: Structure-function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop-loop interaction motif conserved in most natural hammerheads Authors: Dufour, D. / de la Pena, M. / Gago, S. / Flores, R. / Gallego, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rpk.cif.gz | 20.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rpk.ent.gz | 13.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/2rpk ftp://data.pdbj.org/pub/pdb/validation_reports/rp/2rpk | 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: 6421.895 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, restrained energy minimization / Software ordinal: 1 Details: minimized average structure of 33 converged conformers with the least restraint violation energy and total energy | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: minimized average structure of 33 converged conformers with the least restraint violation energy and total energy Conformers calculated total number: 60 / Conformers submitted total number: 1 / Representative conformer: 1 |