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Yorodumi- PDB-6m6j: NMR solution structure of a DNA minidumbbell containing an abasic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m6j | ||||||||||||||||||||
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Title | NMR solution structure of a DNA minidumbbell containing an abasic bulge between two CTTG repeats | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Minidumbbell / Bulge / Abasic site | Function / homology | DNA | Function and homology information Biological species | Homo sapiens (human) | Method | SOLUTION NMR / restrained molecular dynamics | Authors | Wan, L. / Lam, S.L. / Guo, P. | Citation | Journal: Chem.Commun.(Camb.) / Year: 2020 | Title: Rational design of a reversible Mg2+/EDTA-controlled molecular switch based on a DNA minidumbbell. Authors: Wan, L. / 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 | 6m6j.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m6j.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 6m6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m6j_validation.pdf.gz | 315.5 KB | Display | wwPDB validaton report |
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Full document | 6m6j_full_validation.pdf.gz | 383.3 KB | Display | |
Data in XML | 6m6j_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 6m6j_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/6m6j ftp://data.pdbj.org/pub/pdb/validation_reports/m6/6m6j | HTTPS FTP |
-Related structure data
Related structure data | 6m6kC 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: 2588.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
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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: 0.9 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaPi, 99.96% D2O Label: CTTGXCTTG / Solvent system: 99.96% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 10 mM / Ionic strength err: 0.1 / Label: condition_1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 273 K / Temperature err: 0.2 |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: restrained molecular dynamics / Software ordinal: 1 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest total energy Conformers calculated total number: 500 / Conformers submitted total number: 20 |