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 1S0T | pdb_00001s0t

Solution structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate recognition by endonuclease IV


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6100% D2O50 mM NaCl6.6ambient293
2DQF-COSY1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6100% D2O50 mM NaCl6.6ambient293
32D TOCSY1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6100% D2O50 mM NaCl6.6ambient293
42D 31P,1H correlation1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6100% D2O50 mM NaCl6.6ambient293
5HSQC1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6100% D2O50 mM NaCl6.6ambient293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAMX600
2BrukerAVANCE500
NMR Refinement
MethodDetailsSoftware
torsion angle dynamics molecular dynamicsThe structure is based on a total of 502 restraints: 284 distance restraints, 80 endocyclic torsion angle restraints, 50 Watson-Crick distance and angle restraints, and 88 backbone torsion angle restraints. The alphaA duplex structure was elucidated by a combination of DYANA and rMD/rEM in AMBER. All calculations were performed in vacuo. The final structure deposited here was obtained by coordinate averaging the final ensemble of 10 rMD/rEM structures followed by restrained energy minimization.DYANA
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number10
Conformers Submitted Total Number1
Representative Model1 (minimized average structure)
Additional NMR Experimental Information
DetailsFor non-exchangeable protons, NOESY experiments in D2O were performed with 10s relaxation delays and mixing times of 75ms, 150ms and 250 ms. For exchangeable protons, a WATERGATE NOESY was performed with a relaxation delay of 4s and 150ms mixing time.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementDYANA1.5Guntert et al
2refinementAmber6.0Case et al.
3iterative matrix relaxationMARDIGRAS3.2Borgias et al.
4structure solutionCORMA5.2Keepers and James
5structure solutionCurves5.1Lavery and Sklenar
6structure solutionMOLMOL2.0Koradi et al.