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Yorodumi- PDB-2hy9: Human telomere DNA quadruplex structure in K+ solution hybrid-1 form -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hy9 | ||||||
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Title | Human telomere DNA quadruplex structure in K+ solution hybrid-1 form | ||||||
Components | DNA (26-MER) | ||||||
Keywords | DNA / G-quadruplex | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing, molecular dynamics | ||||||
Authors | Dai, J. / Punchihewa, C. / Jones, R.A. / Hurley, L. / Yang, D. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 Title: Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation. Authors: Dai, J. / Punchihewa, C. / Ambrus, A. / Chen, D. / Jones, R.A. / Yang, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hy9.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hy9.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 2hy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/2hy9 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/2hy9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 8236.324 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in Homo sapiens (Human). |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
-Sample preparation
Details | Contents: 0.1-2.5mM oligonucleotide, 25mM phosphate buffer K, 70mM KCl, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 70mM KCl, 25mM K-phosphate / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry simulated annealing, molecular dynamics Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 10 |