2HSK | pdb_00002hsk

NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA100% D2O10 mM sodium phosphate mM6.51 atm298
22D TOCSY2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA100% D2O10 mM sodium phosphate mM6.51 atm298
3E-COSY2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA100% D2O10 mM sodium phosphate mM6.51 atm298
4H-P-selective COSY2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA100% D2O10 mM sodium phosphate mM6.51 atm298
52D NOESY2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA90%H2O/10%D2O (v/v)10 mM sodium phosphate mM6.51 atm277
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1Home-builtCustom-built750
2Home-builtCustom-built591
NMR Refinement
MethodDetailsSoftware
Simulated annealing Molecular dynamicsthe structures are based on 482 NOE-derived distance constraints, 57 dihedral angle restraints,8 distance restraints from hydrogen bonds.Amber
NMR Ensemble Information
Conformer Selection Criteriastructures with the least restraint violations,structures with the lowest energy
Conformers Calculated Total Number30
Conformers Submitted Total Number10
Representative Model1 (minimized average structure)
Additional NMR Experimental Information
DetailsThis structure was determined using standard 2D homonuclear and HP HSQC techniques
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementAmber8.0Case, D.A. et al.
2data analysisFelix2000
3geometry optimizationMARDIGRAS