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- PDB-7e4e: NMR solution structures of DNA minidumbbell containing a N1-methy... -
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Basic information
Entry | Database: PDB / ID: 7e4e | ||||||||||||||||||||
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Title | NMR solution structures of DNA minidumbbell containing a N1-methyladenine | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / DNA minidumbbell / N1-methyladenine / methylation / non-B DNA / Hoogsteen base pair | Function / homology | DNA | ![]() Biological species | ![]() ![]() Method | SOLUTION NMR / simulated annealing | ![]() Wan, L. / Guo, P. / Lam, S.L. | ![]() ![]() Title: Effects of Adenine Methylation on the Structure and Thermodynamic Stability of a DNA Minidumbbell. Authors: Wan, L. / Lam, S.L. / Lee, H.K. / Guo, P. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 31.6 KB | Display | ![]() |
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PDB format | ![]() | 20.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 316.3 KB | Display | ![]() |
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Full document | ![]() | 326.7 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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: 2421.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
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#2: Chemical | ChemComp-NA / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 0.5 mM NA DNA (5'-D(*TP*TP*TP*(MA7)P*TP*TP*TP*A)-3'), 10 mM NA sodium phosphate, 0.02 mM NA DSS, 99.96% D2O Label: 1 / Solvent system: 99.96% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 10 mM / Label: 1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 atm / Temperature: 278 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 | |||||||||
NMR representative | Selection criteria: fewest violations | |||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 5 |