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- PDB-2l7d: Ribonucleotide Perturbation of DNA Structure: Solution Structure ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2l7d | ||||||||||||||||||||
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Title | Ribonucleotide Perturbation of DNA Structure: Solution Structure of [d(CGC)r(G)d(AATTCGCG)]2 | ||||||||||||||||||||
![]() | 5'-D(*![]() DNA / RNA / Ribonucleotide substituted DNA | Function / homology | DNA/RNA hybrid / DNA/RNA hybrid (> 10) | ![]() Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | Model details | lowest energy, model 1 | ![]() DeRose, E.F. / Perera, L. / Murray, M.S. / Kunkel, T.A. / London, R.E. | ![]() ![]() Title: Solution structure of the Dickerson DNA dodecamer containing a single ribonucleotide. Authors: DeRose, E.F. / Perera, L. / Murray, M.S. / Kunkel, T.A. / London, R.E. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 340.7 KB | Display | ![]() |
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Full document | ![]() | 359.1 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 5.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA/RNA hybrid | Mass: 3679.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: rG4 substituted Drew Dickerson dodecamer |
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-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 | Ionic strength: 100 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 212 / Hydrogen bond constraints total count: 92 | ||||||||||||||||||||||||||||||||
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: 5 | ||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.096 Å / Distance rms dev error: 0.02 Å |