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Yorodumi- PDB-5trn: Solution Structure of a DNA Dodecamer with 8-oxoguanine at the 4t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5trn | ||||||||||||||||||||||||||||
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Title | Solution Structure of a DNA Dodecamer with 8-oxoguanine at the 4th position and 5-methylcytosine at the 9th position | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Drew-Dickerson / non-canonical / modified DNA / methylated DNA / epigenetics / CpG site | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / simulated annealing | Authors | Hoppins, J.J. / Gruber, D.R. / Miears, H.L. / Endutkin, A.V. / Zharkov, D.O. / Smirnov, S.L. | Funding support | United States, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2018 | Title: Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation. Authors: Gruber, D.R. / Toner, J.J. / Miears, H.L. / Shernyukov, A.V. / Kiryutin, A.S. / Lomzov, A.A. / Endutkin, A.V. / Grin, I.R. / Petrova, D.V. / Kupryushkin, M.S. / Yurkovskaya, A.V. / Johnson, ...Authors: Gruber, D.R. / Toner, J.J. / Miears, H.L. / Shernyukov, A.V. / Kiryutin, A.S. / Lomzov, A.A. / Endutkin, A.V. / Grin, I.R. / Petrova, D.V. / Kupryushkin, M.S. / Yurkovskaya, A.V. / Johnson, E.C. / Okon, M. / Bagryanskaya, E.G. / Zharkov, D.O. / Smirnov, S.L. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5trn.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5trn.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 5trn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/5trn ftp://data.pdbj.org/pub/pdb/validation_reports/tr/5trn | HTTPS FTP |
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-Related structure data
Related structure data | 5l06C 5l2gC 5uz1C 5uz2C 5uz3C 6alsC 6altC 6aluC 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: 3693.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 50 mM sodium chloride, 10 mM potassium chloride, 0.1 mM EDTA, 1 mM DNA (5'-D(*CP*GP*CP*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*G)-3'), 100% D2O Label: oG4met9 / Solvent system: 100% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | ||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 18 / Conformers submitted total number: 12 |