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Yorodumi- PDB-2jsq: Monomeric Human Telomere DNA Tetraplex with 3+1 Strand Fold Topol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jsq | ||||||
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Title | Monomeric Human Telomere DNA Tetraplex with 3+1 Strand Fold Topology, Two Edgewise Loops and Double-Chain Reversal Loop, Form 2 15BrG, NMR, 10 Structures | ||||||
Components | HUMAN TELOMERE DNA | ||||||
Keywords | DNA / G-TETRAD / 3+1 STRAND FOLDING / EDGEWISE / DOUBLE-CHAIN REVERSAL LOOPS / 10 STRUCTURES / 15BrG Form 2 | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS CARTESIAN DYNAMICS MATRIX RELAXATION | ||||||
Authors | Kuryavyi, V.V. / Phan, A.T. / Luu, K.N. / Patel, D.J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jsq.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jsq.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jsq_validation.pdf.gz | 302.9 KB | Display | wwPDB validaton report |
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Full document | 2jsq_full_validation.pdf.gz | 345.5 KB | Display | |
Data in XML | 2jsq_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 2jsq_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/2jsq ftp://data.pdbj.org/pub/pdb/validation_reports/js/2jsq | HTTPS FTP |
-Related 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: 7974.971 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 / 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 (0.00+-0.00) VS (0.20+-0.42); MAXIMUM VIOLATION (0.00+-0.00) VS (0.25+-0.02); RMSD OF VIOLATIONS (0.02+-0.00) VS (0.02+-0.00); BOND LENGTHS (0.006+-0.000) VS (0.005+-0.000); BOND ANGLES (0.74+-0.01) VS (0.95+-0.02); IMPROPERS (0.38+-0.01) VS (0.44+-0.04); PAIRWISE RMSD: ALL ATOMS (0.68+-0.19) VS (0.80+-0.25); ALL ATOMS EXCEPT T18, T19, A20 (0.45+-0.14) VS (0.49+-0.13). | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 |