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- PDB-1sp6: A DNA duplex containing a cholesterol adduct (alpha-anomer) -

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Basic information

Entry
Database: PDB / ID: 1sp6
TitleA DNA duplex containing a cholesterol adduct (alpha-anomer)
Components
  • 5'-D(*CP*CP*AP*CP*(HOL)P*GP*GP*AP*AP*C)-3'
  • 5'-D(GP*TP*TP*CP*CP*GP*GP*TP*GP*G)-3'
KeywordsDNA / double helix / modified DNA / cholesterol adduct / DNA lesion
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics matrix relaxation
AuthorsGomez-Pinto, I. / Cubero, E. / Kalko, S.G. / Monaco, V. / van der Marel, G. / van Boom, J.H. / Orozco, M. / Gonzalez, C.
CitationJournal: 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
DepositionMar 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*CP*AP*CP*(HOL)P*GP*GP*AP*AP*C)-3'
B: 5'-D(GP*TP*TP*CP*CP*GP*GP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,4682
Polymers6,4682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #5lowest energy

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Components

#1: DNA chain 5'-D(*CP*CP*AP*CP*(HOL)P*GP*GP*AP*AP*C)-3'


Mass: 3375.639 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(GP*TP*TP*CP*CP*GP*GP*TP*GP*G)-3'


Mass: 3092.013 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY

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Sample preparation

DetailsContents: 2mM duplex / Solvent system: 100 mM NaCl, 10 mM phosphate, pH 7
Sample conditionsIonic strength: 100 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA5Gunter, P.structure solution
MARDIGRAS5.2James, T.L.iterative matrix relaxation
XwinNMR1.3Brukercollection
Amber5Kollman, P.A.refinement
XEASY1Bartelsdata analysis
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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