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Yorodumi- PDB-2kow: Structure of a two-G-tetrad basket-type intramolecular G-quadrupl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kow | ||||||||||||||||||||
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Title | Structure of a two-G-tetrad basket-type intramolecular G-quadruplex formed by Giardia telomeric repeat d(TAGGG)4 in K+ solution (with G18-to-INO substitution) | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / telomere / G-quadruplex / G.(A-G) triad / TAGGG repeat / Giardia | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics, matrix relaxation | Model details | lowest energy, model 10 | Authors | Hu, L. / Lim, K.W. / Bouaziz, S. / Phan, A.T. | Citation | Journal: J.Am.Chem.Soc. / Year: 2009 | Title: Giardia Telomeric Sequence d(TAGGG)(4) Forms Two Intramolecular G-Quadruplexes in K(+) Solution: Effect of Loop Length and Sequence on the Folding Topology. Authors: Hu, L. / Lim, K.W. / Bouaziz, S. / Phan, A.T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kow.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kow.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 2kow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/2kow ftp://data.pdbj.org/pub/pdb/validation_reports/ko/2kow | 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: 6360.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Number of used crystals: 1 | ||||||||||||||||||||||||||||||||||||
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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: 90mM K+ / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, molecular dynamics, matrix relaxation Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR constraints | NA chi-angle constraints total count: 8 / NA epsilon-angle constraints total count: 4 / NA other-angle constraints total count: 8 / NOE constraints total: 499 / NOE intraresidue total count: 252 / NOE long range total count: 51 / NOE medium range total count: 31 / NOE sequential total count: 165 / Hydrogen bond constraints total count: 48 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.197 Å / Maximum upper distance constraint violation: 0.237 Å / Representative conformer: 1 | ||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.02 Å / Distance rms dev error: 0.002 Å |