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- PDB-6alt: Solution structure of a DNA dodecamer with 5-methylcytosine at th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6alt | |||||||||||||||||||||||||||||||
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Title | Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 9th position | |||||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Drew-Dickerson / non-canonical / modified DNA / epigenetics | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | SOLUTION NMR / simulated annealing | ![]() Gruber, D.R. / Hoppins, J.J. / Miears, H.L. / Zharkov, D.O. / Smirnov, S.L. | Funding support | | ![]()
![]() ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176 KB | Display | ![]() |
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PDB format | ![]() | 142.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5l06C ![]() 5l2gC ![]() 5trnC ![]() 5uz1C ![]() 5uz2C ![]() 5uz3C ![]() 6alsC ![]() 6aluC C: citing same article ( |
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Similar structure data | |
Other databases |
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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: 3611.466 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 phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*(DC5)P*GP*(DMC)P*GP*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3'), 100% D2O Label: dd06 / Solvent system: 100% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||||||||
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: 11 |