9JX5 | pdb_00009jx5

Solution NMR structure of the 1:1 complex of NOP56 intronic G-quadruplex bound with pyridostatin

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	0.5 mM DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 1.5 mM pyridostatin	99.96% D2O	1 mM	7	1 atm	298	Bruker AVANCE 600
2	2D 1H-1H NOESY	0.5 mM DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 1.5 mM pyridostatin	90% H2O/10% D2O	1 mM	7	1 atm	298	Bruker AVANCE 600
3	2D 1H-1H TOCSY	0.5 mM DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 1.5 mM pyridostatin	99.96% D2O	1 mM	7	1 atm	298	Bruker AVANCE 600
4	2D 1H-1H COSY	0.5 mM DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 1.5 mM pyridostatin	99.96% D2O	1 mM	7	1 atm	298	Bruker AVANCE 600

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

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	500
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	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman