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Yorodumi- PDB-2jsm: MONOMERIC HUMAN TELOMERE DNA TETRAPLEX WITH 3+1 STRAND FOLD TOPOL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jsm | ||||||
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Title | MONOMERIC HUMAN TELOMERE DNA TETRAPLEX WITH 3+1 STRAND FOLD TOPOLOGY, TWO EDGEWISE LOOPS AND DOUBLE-CHAIN REVERSAL LOOP, NMR, 10 STRUCTURES, Form 1 Natural | ||||||
Components | HUMAN TELOMERE DNA | ||||||
Keywords | DNA / G-TETRAD / 3+1 STRAND FOLDING / EDGEWISE / DOUBLE-CHAIN REVERSAL LOOPS / Natural Form 1 / 10 STRUCTURES | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
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 | 2jsm.cif.gz | 144.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jsm.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/2jsm ftp://data.pdbj.org/pub/pdb/validation_reports/js/2jsm | HTTPS FTP |
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-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: 7287.690 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 |
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Sample | Conc.: .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 / 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 (0.3+-0.48) VS (0.00+-0.00) MAXIMUM VIOLATION (0.21+-0.06) VS (0.00+-0.00) RMSD OF VIOLATIONS (0.03+-0.00) VS (0.03+-0.00) BOND LENGTHS (0.004+-0.000) VS (0.004+-0.000) BOND ANGLES (0.71+-0.01) VS (0.92+-0.01) IMPROPERS (0.38+-0.02) VS (0.36+-0.02) PAIRWISE RMSD: ALL ATOMS (0.61+-0.15) VS (0.82+-0.22) ALL ATOMS EXCEPT T6,T7,A8 (0.40+-0.11) VS (0.59+-0.15) | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 |