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- PDB-2hsr: 13mer duplex DNA containing an abasic site with beta anomer -

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Basic information

Entry
Database: PDB / ID: 2hsr
Title13mer duplex DNA containing an abasic site with beta anomer
Components
  • 5'-D(*CP*CP*AP*AP*AP*GP*(AAB)P*AP*CP*CP*GP*GP*G)-3'
  • 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'
KeywordsDNA / abasic site / DNA damage / base excision repair / Ape1
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsChen, J. / Dupradeau, F.Y. / Case, D.A. / Turner, C.J. / Stubbe, J.
CitationJournal: Biochemistry / Year: 2007
Title: Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites.
Authors: Chen, J. / Dupradeau, F.Y. / Case, D.A. / Turner, C.J. / Stubbe, J.
History
DepositionJul 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 9, 2014Group: Non-polymer description
Revision 1.4Aug 8, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Source and taxonomy
Category: ndb_struct_conf_na / ndb_struct_na_base_pair_step ...ndb_struct_conf_na / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _ndb_struct_na_base_pair_step.helical_twist / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ..._ndb_struct_na_base_pair_step.helical_twist / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5May 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*AP*AP*GP*(AAB)P*AP*CP*CP*GP*GP*G)-3'
B: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,8362
Polymers7,8362
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1560 Å2
ΔGint-3 kcal/mol
Surface area5260 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 3877.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'


Mass: 3958.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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
141HP-selective HSQC
2522D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and HP-HSQC heteronuclear techniques

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.7 mM duplex DNA containing an abasic site with beta anomer, 10 mM sodium phosphate, 0.2 mM EDTA, 100% D2Osample_1100% D2O
solution22.7 mM duplex DNA containing an abasic site with beta anomer, 10 mM sodium phosphate, 0.2 mM EDTA, 90% H2O/10%D2O (v/v)sample_290% H2O/10%D2O (v/v)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.7 mMduplex DNA containing an abasic site with beta anomernatural abundance1
2.7 mMduplex DNA containing an abasic site with beta anomernatural abundance2
10 mMsodium phosphatenatural abundance1
10 mMsodium phosphatenatural abundance2
0.2 mMEDTAnatural abundance1
0.2 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mM sodium phosphate mMsample_conditions_16.51 atm298 K
210 mM sodium phosphate mMsample_conditions_26.51 atm277 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built Custom builtHome-builtCustom built7501
Home-built Custom builtHome-builtCustom built5912

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000data analysis
MARDIGRASgeometry optimization
Amber8Case, et al.refinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: the structures are based on 482 NOE-derived distance constraints, 57 dihedral angle restraints,8 distance restraints from hydrogen bonds
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: 10

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