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- PDB-7d0x: NMR solution structures of the DNA minidumbbell formed by 5'-mCTT... -
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Basic information
Entry | Database: PDB / ID: 7d0x | ||||||||||||||||||||
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Title | NMR solution structures of the DNA minidumbbell formed by 5'-mCTTGXmCTTG-3' | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / minidumbbell / 5-methylcytosine / abasic site | Function / homology | DNA | ![]() Biological species | ![]() Method | SOLUTION NMR / restrained molecular dynamics | ![]() Wan, L. / Guo, P. / Lam, S.L. | ![]() ![]() Title: 5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbells. Authors: Wan, L. / Yi, J. / 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 | ![]() | 106 KB | Display | ![]() |
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PDB format | ![]() | 71.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 318.8 KB | Display | ![]() |
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Full document | ![]() | 374.8 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d0yC ![]() 7d0zC C: citing same article ( |
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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: 2536.759 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 DNA (5'-D(*(MC1)P*TP*TP*GP*(DX)P*(DMC)P*TP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS, 99.96% D2O Label: mCTTGX / Solvent system: 99.96% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 25 mM / Label: 1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 atm / Temperature: 273 K / Temperature err: 0.1 |
-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: restrained molecular dynamics / Software ordinal: 2 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 1000 / Conformers submitted total number: 20 |