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- PDB-2hsk: NMR Structure of 13mer Duplex DNA containing an abasic site (Y) i... -

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Basic information

Entry
Database: PDB / ID: 2hsk
TitleNMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)
Components
  • 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)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 lesion / 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 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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 / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _ndb_struct_na_base_pair_step.tip / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ..._ndb_struct_na_base_pair_step.tip / _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
Remark 600HETEROGEN D1P IS AN ALPHA ANOMER. THEREFORE, C1' CENTER HAS CORRECT CHIRALITY AT D1P.

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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*(D1P)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
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1580 Å2
ΔGint-3 kcal/mol
Surface area5230 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*(D1P)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
141H-P-selective COSY
2522D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear and HP HSQC techniques

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA, 100% D2Osample_1100% D2O
solution22.7 mM duplex DNA, 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 DNAnatural abundance1
2.7 mMduplex DNAnatural 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_16.5 1 atm298 K
210 mM sodium phosphate mMsample_conditions_26.5 1 atm277 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
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
Amber8Case, D.A. et al.refinement
FELIX2000data analysis
MARDIGRASgeometry optimization
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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