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Yorodumi- PDB-1tjz: Solution Structure of the Active Site Stem-Loop of the VS Ribozyme -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tjz | ||||||
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Title | Solution Structure of the Active Site Stem-Loop of the VS Ribozyme | ||||||
Components | VS Ribozyme | ||||||
Keywords | RNA / RNA hairpin / RNA stem-loop / protonated adenine / GA base pair | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / The structure calculations utilized standard simulated annealing protocols. | ||||||
Authors | Flinders, J. / Dieckmann, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The solution structure of the VS ribozyme active site loop reveals a dynamic "hot-spot" Authors: Flinders, J. / Dieckmann, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tjz.cif.gz | 272.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tjz.ent.gz | 230.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tjz ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tjz | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 7127.322 Da / Num. of mol.: 1 / Fragment: RNA Loop VI / Source method: obtained synthetically Details: Synthesized enzymatically from a DNA template using T7 polymerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined from restraints derived from homo- and heteronuclear experiments. |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: The structure calculations utilized standard simulated annealing protocols. Software ordinal: 1 Details: The final structures are based on a total of 699 restraints: 582 NOE-derived restraints, 52 dihedral angle restraints, 9 planarity restraints, and 56 distance restraints from hydrogen bonds. | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |