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- PDB-5izp: Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position -
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Open data
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Basic information
Entry | Database: PDB / ID: 5izp | ||||||||||||||||||||
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Title | Solution Structure of DNA Dodecamer with 8-oxoguanine at 10th Position | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Drew-Dickerson / dodecamer / non-canonical / modified DNA / oxidized DNA / DNA damage / DNA adduct / lesion | Function / homology | DNA / DNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | SOLUTION NMR / simulated annealing | ![]() Gruber, D.R. / Hoppins, J.J. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Yurkovskaya, A.V. / Zharkov, D.O. / Smirnov, S.L. | ![]() ![]() Title: 8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme. Authors: Hoppins, J.J. / Gruber, D.R. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Petrova, D.V. / Endutkin, A.V. / Popov, A.V. / Yurkovskaya, A.V. / Fedechkin, S.O. / Brockerman, J.A. / ...Authors: Hoppins, J.J. / Gruber, D.R. / Miears, H.L. / Kiryutin, A.S. / Kasymov, R.D. / Petrova, D.V. / Endutkin, A.V. / Popov, A.V. / Yurkovskaya, A.V. / Fedechkin, S.O. / Brockerman, J.A. / 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 | ![]() | 234 KB | Display | ![]() |
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PDB format | ![]() | 190 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 339.7 KB | Display | ![]() |
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Full document | ![]() | 453.9 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 3679.392 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
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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Processing
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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: 15 |