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Yorodumi- PDB-2koc: NMR solution structure of a 14-mer hairpin RNA with cUUCGg tetraloop -
+Open data
-Basic information
Entry | Database: PDB / ID: 2koc | ||||||||||||||||||||
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Title | NMR solution structure of a 14-mer hairpin RNA with cUUCGg tetraloop | ||||||||||||||||||||
Components | RNA (5'-R(P*Keywords | RNA / UUCG tetraloop / 14-mer hairpin | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | Model details | lowest energy, model 1 | Authors | Nozinovic, S. / Fuertig, B. / Jonker, H.R.A. / Richter, C. / Schwalbe, H. | Citation | Journal: Nucleic Acids Res. / Year: 2009 | Title: High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA Authors: Nozinovic, S. / Furtig, B. / Jonker, H.R.A. / Richter, C. / Schwalbe, H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2koc.cif.gz | 172.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2koc.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 2koc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/2koc ftp://data.pdbj.org/pub/pdb/validation_reports/ko/2koc | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 4454.683 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: High-Resolution NMR Structure of a RNA model system: the 14mer cUUCGg tetraloop hairpin RNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.7mM [U-100% 13C; U-100% 15N] 14-MER RNA-1, 20mM potassium phosphate-2, 0.4mM EDTA-3, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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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, torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 259 / Hydrogen bond constraints total count: 32 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |