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Yorodumi- PDB-2kwg: Solution structure of a fully modified 2'-F/2'-OMe siRNA construct -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kwg | ||||||
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Title | Solution structure of a fully modified 2'-F/2'-OMe siRNA construct | ||||||
Components |
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Keywords | RNA / siRNA / 2'-fluoro / 2'-O-methyl | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Podbevsek, P. / Bhat, B. / Plavec, J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2010 Title: Solution-state structure of a fully alternately 2'-F/2'-OMe modified 42-nt dimeric siRNA construct. Authors: Podbevsek, P. / Allerson, C.R. / Bhat, B. / Plavec, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kwg.cif.gz | 275.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kwg.ent.gz | 238.8 KB | Display | PDB format |
PDBx/mmJSON format | 2kwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kwg_validation.pdf.gz | 352.8 KB | Display | wwPDB validaton report |
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Full document | 2kwg_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 2kwg_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2kwg_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/2kwg ftp://data.pdbj.org/pub/pdb/validation_reports/kw/2kwg | HTTPS FTP |
-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: 6799.100 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 6834.176 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-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 / Software ordinal: 1 Details: 100 ps of NMR restrained simulated annealing calculations using a generalized Born implicit solvation model. | ||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 33 / NA beta-angle constraints total count: 33 / NA chi-angle constraints total count: 42 / NA delta-angle constraints total count: 42 / NA epsilon-angle constraints total count: 33 / NA other-angle constraints total count: 67 | ||||||||||||||||||||
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: 10 |