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Yorodumi- PDB-7zek: Structure of a hybrid-type G-quadruplex with a snapback loop (hyb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zek | ||||||||||||||||||||||||||||
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Title | Structure of a hybrid-type G-quadruplex with a snapback loop (hybrid 1R') | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / hybrid G-quadruplex / snapback loop | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / simulated annealing | Authors | Jana, J. / Vianney, Y.M. / Schroeder, N. / Weisz, K. | Funding support | Germany, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2022 | Title: Guiding the folding of G-quadruplexes through loop residue interactions. Authors: Jana, J. / Vianney, Y.M. / Schroder, N. / Weisz, K. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zek.cif.gz | 144.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zek.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 7zek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/7zek ftp://data.pdbj.org/pub/pdb/validation_reports/ze/7zek | HTTPS FTP |
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-Related structure data
Related structure data | 7zemC 7zeoC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
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: 6928.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 0.3 mM DNA (5'-D(*(DG5)P*GP*CP*TP*AP*(BG)P*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP*TP*CP*AP*(DG3))-3'), 90% H2O/10% D2O Label: sample1 / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.3 mM Component: DNA (5'-D(*(DG5)P*GP*CP*TP*AP*(BG)P*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP*TP*CP*AP*(DG3))-3') Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: 10 mM / Label: sample_1 / pH: 7 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 5 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10 / Conformers submitted total number: 10 |