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- PDB-2kd9: Solution Structure of DNA Containing Alpha-OH-PdG: the Mutagenic ... -

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Basic information

Entry
Database: PDB / ID: 2kd9
TitleSolution Structure of DNA Containing Alpha-OH-PdG: the Mutagenic Adduct Produced by Acrolein
Components
  • 5'-D(*CP*GP*TP*AP*CP*(63G)P*CP*AP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / Acrolein lesions / DNA damaged / DNA structure / exocyclic / Propano-dG lesions
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics
Model detailsminimized average, model 1
Authorsde los Santos, C. / Zaliznyak, T. / Johnson, F. / Bonala, R. / Attaluri, S.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Solution structure of DNA containing alpha-OH-PdG: the mutagenic adduct produced by acrolein.
Authors: Zaliznyak, T. / Bonala, R. / Attaluri, S. / Johnson, F. / de los Santos, C.
History
DepositionJan 5, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*GP*TP*AP*CP*(63G)P*CP*AP*TP*GP*C)-3'
B: 5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,7642
Polymers6,7642
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)26 / 25all calculated structures submitted
RepresentativeModel #1minimized average

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Components

#1: DNA chain 5'-D(*CP*GP*TP*AP*CP*(63G)P*CP*AP*TP*GP*C)-3'


Mass: 3390.249 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3'


Mass: 3374.210 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 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1412D DQF-COSY
2522D 1H-1H NOESY
NMR detailsText: AUTHOR STATES THAT 25 MODELS WERE CALCULATED BY RESTRAINED MD. MODEL 1 IS AN AVERAGED MINIMIZED STRUCTURE OF THESE 25 MODELS.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM DNA duplex, alpha-OH-PdG-1, 100% D2O100% D2O
22.5 mM DNA duplex, alpha-OH-PdG-2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2.5 mMDNA duplex, alpha-OH-PdG-11
2.5 mMDNA duplex, alpha-OH-PdG-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl 5.9ambient 298 K
250mM NaCl 5.9ambient 278 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.data analysis
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.peak picking
VNMRVariancollection
Insight IIAccelrys Software Inc.geometry optimization
ChimeraUCSF Chimerageometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 16 / NA beta-angle constraints total count: 16 / NA chi-angle constraints total count: 16 / NA delta-angle constraints total count: 16 / NA epsilon-angle constraints total count: 16 / NA gamma-angle constraints total count: 16 / NOE constraints total: 485 / Hydrogen bond constraints total count: 26
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 25 / Conformers submitted total number: 26 / Maximum lower distance constraint violation: 0.6 Å / Maximum upper distance constraint violation: 0.6 Å
NMR ensemble rmsDistance rms dev: 0.3 Å

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