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Yorodumi- PDB-6rio: Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3') -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rio | ||||||||||||||||||||||||||||||||||
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Title | Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3') | ||||||||||||||||||||||||||||||||||
Components | DNA (5'-(*Keywords | DNA / Polyamide / Minor groove binder | Function / homology | Chem-K4Z / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / molecular dynamics / matrix relaxation | Authors | Padroni, G. / Withers, J.M. / Taladriz-Sender, A. / Reichenbach, L.F. / Parkinson, J.A. / Burley, G.A. | Funding support | United Kingdom, 3items |
Citation | Journal: J.Am.Chem.Soc. / Year: 2019 | Title: Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components. Authors: Padroni, G. / Withers, J.M. / Taladriz-Sender, A. / Reichenbach, L.F. / Parkinson, J.A. / Burley, G.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rio.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rio.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rio_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 6rio_full_validation.pdf.gz | 481.6 KB | Display | |
Data in XML | 6rio_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6rio_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/6rio ftp://data.pdbj.org/pub/pdb/validation_reports/ri/6rio | HTTPS FTP |
-Related structure data
Related structure data | 6i4nC 6i4oC 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: 3582.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K4Z / | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 100 mM / Label: Conditions 1 / pH: 7.45 / Pressure: 1 atm / Temperature: 298 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 |
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NMR representative | Selection criteria: closest to the average | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 2000 / Conformers submitted total number: 10 |