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Yorodumi- PDB-6i4n: Dodecamer DNA containing the synthetic base pair P-Z in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i4n | ||||||||||||||||||||
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Title | Dodecamer DNA containing the synthetic base pair P-Z in complex with a pyrrole-imidazole polyamide | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / synthetic base pair / Z / P / pyrrole-imidazole polyamide | Function / homology | Chem-K4Z / DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | SOLUTION NMR / simulated annealing / molecular dynamics | Authors | Padroni, G. / Parkison, J. / Burley, G.A. | 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 | 6i4n.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i4n.ent.gz | 156.9 KB | Display | PDB format |
PDBx/mmJSON format | 6i4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i4n_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 6i4n_full_validation.pdf.gz | 500.2 KB | Display | |
Data in XML | 6i4n_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6i4n_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/6i4n ftp://data.pdbj.org/pub/pdb/validation_reports/i4/6i4n | HTTPS FTP |
-Related structure data
Related structure data | 6i4oC 6rioC 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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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3706.414 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: D2O / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement |
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NMR representative | Selection criteria: most represented cluster | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 5000 / Conformers submitted total number: 10 |