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Yorodumi- PDB-1pyj: Solution Structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine add... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pyj | ||||||
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Title | Solution Structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11mer DNA duplex | ||||||
Components |
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Keywords | DNA / DNA Adduct | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / molecular mechanics in torsion angle space | ||||||
Model type details | minimized average | ||||||
Authors | Peterson, L.A. / Vu, C. / Hingerty, B.E. / Broyde, S. / Cosman, M. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Solution structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11 mer DNA duplex: evidence for formation of a base triplex. Authors: Peterson, L.A. / Vu, C. / Hingerty, B.E. / Broyde, S. / Cosman, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pyj.cif.gz | 20.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pyj.ent.gz | 15.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/1pyj ftp://data.pdbj.org/pub/pdb/validation_reports/py/1pyj | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 3441.336 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3414.234 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: This structure was determined using standard 2D homonuclear techniques |
-Sample preparation
Details | Contents: 1 mM [POB]dG-dC 11mer duplex adduct in 600 ul 10 mM sodium phosphate, 0.1 M NaCl, 0.1 mM EDTA, pH7.0 Solvent system: 100% D2O and 90% H2O, 10% D2O |
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Sample conditions | Ionic strength: 0.1 M NaCl / pH: 7.00 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: molecular mechanics in torsion angle space / Software ordinal: 1 Details: The structures are based on a total of 325 restraints (271 DNA-DNA, 22 POB-DNA, 5 POB-POB, 29 H-bonds). | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |