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- PDB-2hli: Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methy... -

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Basic information

Entry
Database: PDB / ID: 2hli
TitleSolution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence
Components
  • DNA dodecamer
  • DNA dodecamer with S-crotonaldehyde adduct
KeywordsDNA / Interstrand DNA cross-link / S-crotonaldehyde-dG adduct / 5'-CpG-3' sequence
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics matrix relaxation, torsion angle
Model type detailsminimized average
AuthorsCho, Y.-J. / Wang, H. / Kozekov, I.D. / Kurtz, A.J. / Jacob, J. / Voehler, M. / Smith, J. / Harris, T.M. / Rizzo, C.J. / Stone, M.P.
CitationJournal: Chem.Res.Toxicol. / Year: 2006
Title: Orientation of the Crotonaldehyde-Derived N(2)-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct Hinders Interstrand Cross-Link Formation in the 5'-CpG-3' Sequence
Authors: Cho, Y.-J. / Wang, H. / Kozekov, I.D. / Kozekova, A. / Kurtz, A.J. / Jacob, J. / Voehler, M. / Smith, J. / Harris, T.M. / Rizzo, C.J. / Lloyd, R.S. / Stone, M.P.
History
DepositionJul 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA dodecamer with S-crotonaldehyde adduct
B: DNA dodecamer


Theoretical massNumber of molelcules
Total (without water)7,3972
Polymers7,3972
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #10minimized average structure

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Components

#1: DNA chain DNA dodecamer with S-crotonaldehyde adduct


Mass: 3733.482 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: All adducted sequences were made by Dr. Rizzo and Dr. Harris lab at Vanderbilt
#2: DNA chain DNA dodecamer


Mass: 3663.392 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
222DQF-COSY
333E-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1 mM in 0.25 mL; 10 mM Sodium phosphate buffer; 0.1 M NaCl; 50 uMNa2EDTA
Solvent system: 99.996% D2O
Sample conditionsIonic strength: 0.1 M NaCl / pH: 9.3 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance6002
Bruker AvanceBrukerAvance5003

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR3.5Brukercollection
NMRPipe2.3Delaglio F et al.processing
FELIX2000Accelrys, Inc.data analysis
MARDIGRAS5.2.1Keepers, JW et al.iterative matrix relaxation
AMBER8Case et alrefinement
CORMA5.2Keepers JW et al.data analysis
RefinementMethod: distance geometry simulated annealing, molecular dynamics matrix relaxation, torsion angle
Software ordinal: 1
Details: 308 distance restraints, 90 sugar pucker restraints, 52 H-bonding restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 1

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