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Yorodumi- PDB-2jyj: Re-refining the tetraloop-receptor RNA-RNA complex using NMR-deri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jyj | ||||||
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Title | Re-refining the tetraloop-receptor RNA-RNA complex using NMR-derived restraints and Xplor-nih (2.18) | ||||||
Components | RNA (43-MER) | ||||||
Keywords | RNA/RNA / RNA structure / RNA-RNA complex / tetraloop-receptor / GAAA-tetraloop / RNA global structure | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Zuo, X. / Wang, J. / Foster, T.R. / Schwieters, C.D. / Tiede, D.M. / Butcher, S.E. / Wang, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. Authors: Davis, J.H. / Tonelli, M. / Scott, L.G. / Jaeger, L. / Williamson, J.R. / Butcher, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jyj.cif.gz | 525.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jyj.ent.gz | 447.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/2jyj ftp://data.pdbj.org/pub/pdb/validation_reports/jy/2jyj | 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: 13873.258 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 1H-13C NOESY |
-Sample preparation
Details | Contents: 8 mg/ml (w/v) Tetraloop-receptor RNA/RNA complex, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 8 w/v Component: Tetraloop-receptor RNA:RNA complex RNA-RNA complex |
Sample conditions | Ionic strength: 20 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
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-Processing
NMR software | Name: X-PLOR NIH / Version: 2.18 / Developer: Schwieters, C.D. et al. / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: This ensemble of the structures were re-refined with NMR-derived restraints. The original refinements have been published in JMB (2005, 351(2), pp351-82). We re-refined the structures of the ...Details: This ensemble of the structures were re-refined with NMR-derived restraints. The original refinements have been published in JMB (2005, 351(2), pp351-82). We re-refined the structures of the tetraloop-receptor RNA/RNA complex using the restraint files whose formats are consistent with Xplor-nih. No SAXS data was used in this refinement. |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |