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Yorodumi- PDB-1rde: NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rde | ||||||
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Title | NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+ | ||||||
Components | Thrombin-binding DNA aptamer | ||||||
Keywords | DNA / thrombin-binding DNA / Sr2+ / quadruplex | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model type details | minimized average | ||||||
Authors | Mao, X. / Marky, L.A. / Gmeiner, W.H. | ||||||
Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2004 Title: NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+. Authors: Mao, X. / Marky, L.A. / Gmeiner, W.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rde.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rde.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rde ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rde | 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: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: this sequence was seleted from 10^13 DNA |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: >3mM / pH: 4.7 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 11 / Conformers submitted total number: 11 |