[English] 日本語
Yorodumi- PDB-7d0x: NMR solution structures of the DNA minidumbbell formed by 5'-mCTT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d0x | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | NMR solution structures of the DNA minidumbbell formed by 5'-mCTTGXmCTTG-3' | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / minidumbbell / 5-methylcytosine / abasic site | Function / homology | DNA | Function and homology information Biological species | Homo sapiens (human) | Method | SOLUTION NMR / restrained molecular dynamics | Authors | Wan, L. / Guo, P. / Lam, S.L. | Citation | Journal: Chemistry / Year: 2021 | Title: 5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbells. Authors: Wan, L. / Yi, J. / Lam, S.L. / Lee, H.K. / Guo, P. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7d0x.cif.gz | 106 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7d0x.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 7d0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d0x_validation.pdf.gz | 318.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7d0x_full_validation.pdf.gz | 374.8 KB | Display | |
Data in XML | 7d0x_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 7d0x_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/7d0x ftp://data.pdbj.org/pub/pdb/validation_reports/d0/7d0x | HTTPS FTP |
-Related structure data
Related structure data | 7d0yC 7d0zC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 2536.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
---|---|---|---|
#2: Chemical | ChemComp-NA / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Type: solution Contents: 0.5 mM DNA (5'-D(*(MC1)P*TP*TP*GP*(DX)P*(DMC)P*TP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS, 99.96% D2O Label: mCTTGX / Solvent system: 99.96% D2O | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||
Sample conditions | Ionic strength: 25 mM / Label: 1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 atm / Temperature: 273 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
---|
-Processing
NMR software |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: restrained molecular dynamics / Software ordinal: 2 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 1000 / Conformers submitted total number: 20 |