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Yorodumi- PDB-7d0y: NMR solution structures of the DNA minidumbbell formed by two CmC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d0y | ||||||||||||||||||||
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Title | NMR solution structures of the DNA minidumbbell formed by two CmCTG repeats at pH 5 | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / minidumbbell / methylation / CCTG / 5-methylcytosine / pH 5 | Function / homology | DNA | Function and homology information Biological species | Homo sapiens (human) | Method | SOLUTION NMR / restrained molecular dynamics | Authors | Wan, L. / Guo, P. / Lam, S.L. | Citation | Journal: Chemistry / Year: 2021 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d0y.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d0y.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 7d0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/7d0y ftp://data.pdbj.org/pub/pdb/validation_reports/d0/7d0y | HTTPS FTP |
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-Related structure data
Related structure data | 7d0xC 7d0zC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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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: 2326.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
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#2: Chemical | ChemComp-NA / Compound details | DCZ (A 1), 5CM (A 2) have extra atom H3 as N3-site protonated. | 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: 0.2 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaCl, 99.96% D2O Label: CmCTG2, pH 5, D2O / Solvent system: 99.96% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 10 mM / Label: pH 5 / pH: 5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 273 K |
-NMR measurement
NMR spectrometer |
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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: 500 / Conformers submitted total number: 20 |