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Yorodumi- PDB-2mo2: Solution NMR structure of DNA dodecamer containing the 5-hydroxyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mo2 | ||||||||||||||||||||||
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Title | Solution NMR structure of DNA dodecamer containing the 5-hydroxycytosine | ||||||||||||||||||||||
Components | DNA_(5'-D(*Keywords | DNA / 5-hydroxycytosine | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Model details | minimized average structure, model1 | Model type details | minimized average | Authors | Donahue, P.S. / Szulik, M.W. / Stone, M.P. | Citation | Journal: To be Published | Title: Characterization of 5-hydroxycytosine in DNA Authors: Szulik, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mo2.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mo2.ent.gz | 141.3 KB | Display | PDB format |
PDBx/mmJSON format | 2mo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/2mo2 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/2mo2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 100 mM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5OC)P*GP*CP*G)-3'), 100 % D2O, 10 mM sodium phosphate, 100 mM sodium chloride, 11 mM sodium azide, 0.05 mM EDTA, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||||||||
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Sample |
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Sample conditions | pH: 7 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
NMR spectrometer | Type: Bruker INOVA / Manufacturer: Bruker / Model: INOVA / Field strength: 900 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: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 40 / Conformers submitted total number: 11 |