+Open data
-Basic information
Entry | Database: PDB / ID: 1rvh | ||||||||||||||||||
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Title | SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing, for details see (Padrta et al. (2002) J. Biomol. NMR 24, 1-24) | Authors | Stefl, R. / Wu, H. / Ravindranathan, S. / Sklenar, V. / Feigon, J. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 | Title: DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum. Authors: Stefl, R. / Wu, H. / Ravindranathan, S. / Sklenar, V. / Feigon, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rvh.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rvh.ent.gz | 118 KB | Display | PDB format |
PDBx/mmJSON format | 1rvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/1rvh ftp://data.pdbj.org/pub/pdb/validation_reports/rv/1rvh | 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: DNA chain | Mass: 3661.416 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 |
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NMR details | Text: THIS STRUCTURE WAS DETERMINED USING RESIDUAL DIPOLAR COUPLINGS |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 25 mM NH4Cl / pH: 6.0 / Pressure: ambient / Temperature: 288 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software | Name: Amber / Version: 7 / Developer: CASE, D.A., et al. / Classification: refinement |
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Refinement | Method: simulated annealing, for details see (Padrta et al. (2002) J. Biomol. NMR 24, 1-24) Software ordinal: 1 Details: the structures are based on a total of 870 restraints, 586 are NOE-derived distance restraints, 160 torsion angle restraints, 24 pseudorotation phase angle restraints, 24 distance restraints ...Details: the structures are based on a total of 870 restraints, 586 are NOE-derived distance restraints, 160 torsion angle restraints, 24 pseudorotation phase angle restraints, 24 distance restraints from W-C hydrogen bonds. |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 9 |