9KTJ | pdb_00009ktj

Solution NMR structures of ATP-binding DNA aptamer in complex with ATP

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS	99.96%D2O	70 mM	7	1 atm	293	Bruker AVANCE 600
4	2D 1H-1H NOESY	0.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS	90% H2O/10% D2O	70 mM	7	1 atm	293	Bruker AVANCE 600
2	2D 1H-1H COSY	0.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS	99.96%D2O	70 mM	7	1 atm	293	Bruker AVANCE 600
3	2D 1H-1H TOCSY	0.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS	99.96%D2O	70 mM	7	1 atm	293	Bruker AVANCE 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
simulated annealing		GROMACS
energy minimization		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	TopSpin		Bruker Biospin
2	structure calculation	GROMACS		GROMACS development team
3	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman