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- PDB-2jsk: Monomeric Human Telomere DNA Tetraplex with 3+1 Strand Fold Topol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jsk | ||||||
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Title | Monomeric Human Telomere DNA Tetraplex with 3+1 Strand Fold Topology, Two Edgewise Loops and Double-Chain Reversal Loop, 16 G Form 1, NMR, 10 Structures | ||||||
![]() | HUMAN TELOMERE DNA | ||||||
![]() | DNA / G-TETRAD / 3+1 STRAND FOLDING / EDGEWISE / DOUBLE-CHAIN REVERSAL LOOPS / Form 1 16BrG / 10 STRUCTURES | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS CARTESIAN DYNAMICS MATRIX RELAXATION | ||||||
![]() | Kuryavyi, V.V. / Phan, A.T. / Luu, K.N. / Patel, D.J. | ||||||
![]() | ![]() Title: Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Authors: Phan, A.T. / Kuryavyi, V. / Luu, K.N. / Patel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.9 KB | Display | ![]() |
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PDB format | ![]() | 120.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 301.6 KB | Display | ![]() |
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Full document | ![]() | 348.1 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 5.9 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: 7366.586 Da / Num. of mol.: 1 / 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: 0.5-5.0 mM HUMAN TELOMERE DNA, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: HUMAN TELOMERE DNA |
Sample conditions | Ionic strength: 70 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS CARTESIAN DYNAMICS MATRIX RELAXATION Software ordinal: 1 Details: AFTER DEPOSITION, THE MOLECULES WERE ENERGY MINIMIZED WITH THE ENERGY FUNCTION IMPLEMENTING GEOMETRICAL VALUES IN EFFECT AT RCSB SINCE JULY 31 2007. AS A RESULT, STRUCTURE STATISTICS FOR ...Details: AFTER DEPOSITION, THE MOLECULES WERE ENERGY MINIMIZED WITH THE ENERGY FUNCTION IMPLEMENTING GEOMETRICAL VALUES IN EFFECT AT RCSB SINCE JULY 31 2007. AS A RESULT, STRUCTURE STATISTICS FOR THIS ENTRY SLIGHTLY DEVIATES FROM THE PUBLISHED ONE, AS FOLLOWS (CURRENT VS PUBLISHED): NOE VIOLATIONS (>0.2) (0.3+-0.48) VS (0.10+-0.32); MAXIMUM VIOLATION (0.20+-0.00) VS (0.21+-0.07); RMSD OF VIOLATIONS (0.03+-0.02) VS (0.02+-0.00); BOND LENGTHS (0.005+-0.000) VS (0.004+-0.000); BOND ANGLES (0.70+-0.01) VS (0.93+-0.02); IMPROPERS (0.31+-0.01) VS (0.32+-0.02); PAIRWISE RMSD: ALL ATOMS (0.78+-0.29) VS (0.67+-0.22); ALL ATOMS EXCEPT T6,T7,A8 (0.57+-0.22) VS (0.53+-0.15). | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 100 / Conformers submitted total number: 10 |