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Yorodumi- PDB-7ohm: A self-complementary DNA dodecamer duplex contaning 5-hydroxymeth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ohm | |||||||||||||||||||||||||||||||
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Title | A self-complementary DNA dodecamer duplex contaning 5-hydroxymethylcitosine | |||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / 5-hydroxymethylcitosine / Chemically modified DNA / DNA duplex / Epigenetics | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / molecular dynamics | Authors | Battistini, F. / Dans, P.D. / Terrazas, M. / Castellazzi, C.L. / Portella, G. / Labrador, M. / Villegas, N. / Brun-Heath, I. / Gonzalez, C. / Orozco, M. | Funding support | Spain, 2items |
Citation | Journal: Plos Comput.Biol. / Year: 2021 | Title: The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. Authors: Battistini, F. / Dans, P.D. / Terrazas, M. / Castellazzi, C.L. / Portella, G. / Labrador, M. / Villegas, N. / Brun-Heath, I. / Gonzalez, C. / Orozco, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ohm.cif.gz | 117.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ohm.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ohm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ohm_validation.pdf.gz | 408.2 KB | Display | wwPDB validaton report |
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Full document | 7ohm_full_validation.pdf.gz | 729.6 KB | Display | |
Data in XML | 7ohm_validation.xml.gz | 48.7 KB | Display | |
Data in CIF | 7ohm_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/7ohm ftp://data.pdbj.org/pub/pdb/validation_reports/oh/7ohm | HTTPS FTP |
-Related structure data
Related structure data | 7ogvC 7oheC 7ohjC 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: 2457.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) Has ligand of interest | Y | |
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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: 1 mM DNA (5'-D(*CP*GP*AP*(DH)P*GP*TP*CP*G)-3'), 90% H2O/10% D2O Label: unlabelled / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1 mM / Component: DNA (5'-D(*CP*GP*AP*(DH)P*GP*TP*CP*G)-3') / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 125 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 278 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 2 | |||||||||||||||
NMR representative | Selection criteria: none | |||||||||||||||
NMR ensemble | Conformer selection criteria: none / Conformers calculated total number: 10 / Conformers submitted total number: 10 |