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- PDB-1pyj: Solution Structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine add... -

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Entry
Database: PDB / ID: 1pyj
TitleSolution Structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11mer DNA duplex
Components
  • 5'-D(*CP*CP*AP*TP*AP*TP*GP*GP*CP*CP*C)-3'
  • 5'-D*GP*GP*GP*CP*CP*AP*TP*AP*TP*GP*G)-3'
KeywordsDNA / DNA Adduct
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular mechanics in torsion angle space
Model type detailsminimized average
AuthorsPeterson, L.A. / Vu, C. / Hingerty, B.E. / Broyde, S. / Cosman, M.
CitationJournal: 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
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 6, 2014Group: Non-polymer description
Revision 1.4May 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,8562
Polymers6,8562
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)1 / -
Representativeminimized average structure

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Components

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


Mass: 3441.336 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D*GP*GP*GP*CP*CP*AP*TP*AP*TP*GP*G)-3'


Mass: 3414.234 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 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
Sample conditionsIonic strength: 0.1 M NaCl / pH: 7 / Pressure: ambient / Temperature: 298 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
Felix97Accerylsdata analysis
DUPLEXHingerty and Broydestructure solution
DUPLEXHingerty and Broyderefinement
RefinementMethod: 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 representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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