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Open data
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Basic information
Entry | Database: PDB / ID: 2k8z | ||||||||||||||||||
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Title | Dimeric solution structure of the DNA loop d(TCGTTGCT) | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / quadruplex / DNA-loop / minor groove tetrad | Function / homology | DNA | ![]() Method | SOLUTION NMR / molecular dynamics | ![]() Viladoms, J. / Escaja, N. / Frieden, M. / Gomez-Pinto, I. / Pedroso, E. / Gonzalez, C. | ![]() ![]() Title: Self-association of short DNA loops through minor groove C:G:G:C tetrads. Authors: Viladoms, J. / Escaja, N. / Frieden, M. / Gomez-Pinto, I. / Pedroso, E. / Gonzalez, C. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.4 KB | Display | ![]() |
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PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 320.2 KB | Display | ![]() |
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Full document | ![]() | 374.3 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 chain | Mass: 2408.589 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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Sample preparation
Details | Contents: 0.1-2.0 mM DNA (5'-D(*DTP*DCP*DGP*DTP*DTP*DGP*DCP*DT)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 10 mM magnesium chloride, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||||||||||||
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Sample |
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Sample conditions | pH: 7 / Pressure: ambient / Temperature: 278 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |