+Open data
-Basic information
Entry | Database: PDB / ID: 1sp6 | ||||||
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Title | A DNA duplex containing a cholesterol adduct (alpha-anomer) | ||||||
Components |
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Keywords | DNA / double helix / modified DNA / cholesterol adduct / DNA lesion | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | SOLUTION NMR / molecular dynamics matrix relaxation | ||||||
Authors | Gomez-Pinto, I. / Cubero, E. / Kalko, S.G. / Monaco, V. / van der Marel, G. / van Boom, J.H. / Orozco, M. / Gonzalez, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Effect of bulky lesions on DNA: Solution structure of a DNA duplex containing a cholesterol adduct. Authors: Gomez-Pinto, I. / Cubero, E. / Kalko, S.G. / Monaco, V. / Van Der Marel, G. / Van Boom, J.H. / Orozco, M. / Gonzalez, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sp6.cif.gz | 151.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sp6.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 1sp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sp6_validation.pdf.gz | 323.7 KB | Display | wwPDB validaton report |
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Full document | 1sp6_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 1sp6_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 1sp6_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/1sp6 ftp://data.pdbj.org/pub/pdb/validation_reports/sp/1sp6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3375.639 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3092.013 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 2mM duplex / Solvent system: 100 mM NaCl, 10 mM phosphate, pH 7 |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 278 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: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: molecular dynamics matrix relaxation / Software ordinal: 1 Details: The structures are based on a total of 311 NOE-derived distance constraints obtained from a complete relaxation matrix refinement. The structures were calculated by using restrained ...Details: The structures are based on a total of 311 NOE-derived distance constraints obtained from a complete relaxation matrix refinement. The structures were calculated by using restrained molecular dynamics with explicit solvent, and applying the particle Mesh Ewald method | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |