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- PDB-2o7y: Duplex DNA containing an abasic site with an opposite T (alpha an... -

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Basic information

Entry
Database: PDB / ID: 2o7y
TitleDuplex DNA containing an abasic site with an opposite T (alpha anomer) in 5'-G_AC-3' (10 structure ensemble and averaged structure)
Components
  • 5'-D(*CP*CP*AP*AP*AP*GP*(ORP)P*AP*CP*CP*GP*GP*G)-3'
  • 5'-D(*CP*CP*CP*GP*GP*TP*TP*CP*TP*TP*TP*GP*G)-3'
KeywordsDNA / DNA damage / APE1 / abasic / AMBER / molecular dynamics
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics matrix relaxation
Model type detailsminimized average
AuthorsDupradeau, F.Y. / Case, D.A. / Turner, C.J. / Stubbe, J.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics.
Authors: Chen, J. / Dupradeau, F.Y. / Case, D.A. / Turner, C.J. / Stubbe, J.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_database_related
Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,8272
Polymers7,8272
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 30structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #11minimized average structure

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Components

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


Mass: 3877.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized.
#2: DNA chain 5'-D(*CP*CP*CP*GP*GP*TP*TP*CP*TP*TP*TP*GP*G)-3'


Mass: 3949.557 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
1212D TOCSY
131E-COSY
141H-P HSQC
151H3'-selective HSQC
262WATERGATE-NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and H-P heteronuclear experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
12.7 mM duplex DNA100% D2O
22.7 mM duplex DNA90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM Sodium Phosphate, 0.2 mM EDTA 6.5 1 atm298 K
210 mM Sodium Phosphate, 0.2 mM EDTA 6.5 1 atm277 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Custom-built Custom built / Manufacturer: Custom-built / Model: Custom built / Field strength: 591 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2001Accelrys Inc.data analysis
MARDIGRASJamesiterative matrix relaxation
Amber8Case et al.structure solution
Amber8Case et al.refinement
RefinementMethod: simulated annealing, molecular dynamics matrix relaxation
Software ordinal: 1
Details: the structures are based on 452 NOE-derived distance constraints, 62 dihedral angle restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 11

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