[English] 日本語
Yorodumi- PDB-1ow9: NMR Structure of the Active Conformation of the VS Ribozyme Cleav... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ow9 | ||||||
---|---|---|---|---|---|---|---|
Title | NMR Structure of the Active Conformation of the VS Ribozyme Cleavage Site | ||||||
Components | A mimic of the VS Ribozyme Hairpin Substrate | ||||||
Keywords | RNA / VS ribozyme / substrate hairpin / cleavage site / sheared G-A base pairs / shared sheared G-A base pairs / magnesium ion binding / GNRA tetraloop / riboze zipper | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / restrained molecular dynamics; simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Hoffmann, B. / Mitchell, G.T. / Gendron, P. / Major, F. / Andersen, A.A. / Collins, R.A. / Legault, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: NMR Structure of the Active Conformation of the Varkud satellite Ribozyme Cleavage Site Authors: Hoffmann, B. / Mitchell, G.T. / Gendron, P. / Major, F. / Andersen, A.A. / Collins, R.A. / Legault, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ow9.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ow9.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ow9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/1ow9 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/1ow9 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: RNA chain | Mass: 7488.577 Da / Num. of mol.: 1 / Fragment: VS RNA substrate hairpin / Source method: obtained synthetically Details: This sequence is derived from the Neurospora VS ribozyme substrate |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||
NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: 50mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K | |||||||||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: restrained molecular dynamics; simulated annealing / Software ordinal: 1 Details: the first model is the minimized average structure, the last 10 represent the ensemble of structures | ||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 11 |