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Yorodumi- PDB-2akg: Thallium form of the G-Quadruplex from Oxytricha Nova, d(G4T4G4)2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2akg | ||||||||||||||||||
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Title | Thallium form of the G-Quadruplex from Oxytricha Nova, d(G4T4G4)2 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Deoxyribonucleic acid / G-Quadruplex / Thallium | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / (1) distance geometry with simulated annealing; (2) torsion angle dynamics (2000 K for 60 ps with 15 fs timesteps); (3) cartesian dynamics (1000 K for 5 ps with 5 fs timesteps); (4) restrained molecular dynamics (100 cycles of 200 steps each) | Authors | Gill, M.L. / Strobel, S.A. / Loria, J.P. | Citation | Journal: J.Am.Chem.Soc. / Year: 2005 | Title: (205)Tl NMR methods for the characterization of monovalent cation binding to nucleic acids Authors: Gill, M.L. / Strobel, S.A. / Loria, J.P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2akg.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2akg.ent.gz | 126.2 KB | Display | PDB format |
PDBx/mmJSON format | 2akg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/2akg ftp://data.pdbj.org/pub/pdb/validation_reports/ak/2akg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Sequence obtained from Sterkiella nova (Oxytricha nova) telomere |
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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 without the use of isotopically enriched nucleotides. |
-Sample preparation
Details |
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Sample conditions |
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-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 |
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Refinement | Method: (1) distance geometry with simulated annealing; (2) torsion angle dynamics (2000 K for 60 ps with 15 fs timesteps); (3) cartesian dynamics (1000 K for 5 ps with 5 fs timesteps); (4) ...Method: (1) distance geometry with simulated annealing; (2) torsion angle dynamics (2000 K for 60 ps with 15 fs timesteps); (3) cartesian dynamics (1000 K for 5 ps with 5 fs timesteps); (4) restrained molecular dynamics (100 cycles of 200 steps each) Software ordinal: 1 | ||||||||||||||||||||||||||||
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 |