+Open data
-Basic information
Entry | Database: PDB / ID: 1d3x | ||||||
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Title | INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES | ||||||
Components |
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Keywords | DNA / OLIGONUCLEOTIDE / TRIPLEX / RNA THIRD STRAND | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING | ||||||
Authors | Tarkoy, M. / Phipps, A.K. / Schultze, P. / Feigon, J. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT). Authors: Tarkoy, M. / Phipps, A.K. / Schultze, P. / Feigon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d3x.cif.gz | 160.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d3x.ent.gz | 129.3 KB | Display | PDB format |
PDBx/mmJSON format | 1d3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d3x ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d3x | 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: 2508.694 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 AND BETWEEN T 16 AND T 17, C 18, C 20, AND C 22 ARE PROTONATED AT N3 |
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#2: DNA chain | Mass: 2343.552 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 AND BETWEEN T 16 AND T 17, C 18, C 20, AND C 22 ARE PROTONATED AT N3 |
#3: DNA chain | Mass: 2343.552 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A 8 AND T 9 AND BETWEEN T 16 AND T 17, C 18, C 20, AND C 22 ARE PROTONATED AT N3 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 5.7 / Temperature: 303 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 Details: LAST REFINEMENT STEP USED RELAXATION MATRIX REFINEMENT. | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST OVERALL ENERGY / Conformers calculated total number: 20 / Conformers submitted total number: 10 |