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Yorodumi- PDB-6m0b: Solution NMR structures of DNA minidumbbell formed by 5'-CTTG CGTG-3'. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m0b | ||||||||||||||||||||
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Title | Solution NMR structures of DNA minidumbbell formed by 5'-CTTG CGTG-3'. | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / DNA structure / minidumbbell / type II tetraloop | Function / homology | DNA | Function and homology information Biological species | Homo sapiens (human) | Method | SOLUTION NMR / simulated annealing | Authors | Ngai, C.K. / Guo, P. | Citation | Journal: J.Phys.Chem.B / Year: 2020 | Title: High-Resolution Structures of DNA Minidumbbells Comprising Type II Tetraloops with a Purine Minor Groove Residue. Authors: Ngai, C.K. / Lam, S.L. / Lee, H.K. / Guo, P. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m0b.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m0b.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 6m0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m0b_validation.pdf.gz | 315.8 KB | Display | wwPDB validaton report |
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Full document | 6m0b_full_validation.pdf.gz | 405.7 KB | Display | |
Data in XML | 6m0b_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 6m0b_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/6m0b ftp://data.pdbj.org/pub/pdb/validation_reports/m0/6m0b | HTTPS FTP |
-Related structure data
Related structure data | 6m0cC 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: 2433.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||
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#2: Chemical | ChemComp-NA / Has ligand of interest | N | |
-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*TP*TP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS, 99.96% D2O Label: MDB_G6 / Solvent system: 99.96% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 10 NaPi mM / Label: Normal condition / pH: 7.0 / Pressure: 1 atm / Temperature: 278 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 |