6V0L | pdb_00006v0l

PDGFR-b Promoter Forms a G-Vacancy Quadruplex that Can be Complemented by dGMP: Molecular Structure and Recognition of Guanine Derivatives and Metabolites

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H TOCSY	3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP)	90% H2O/10% D2O	50 mM	7	760 mmHg	278	Bruker AVANCE III 800
2	2D 1H-1H NOESY	3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP)	90% H2O/10% D2O	50 mM	7.0	760 mmHg	288	Bruker AVANCE III 800
6	2D 1H-1H NOESY	3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP)	90% H2O/10% D2O	50 mM	7	760 mmHg	298	Bruker AVANCE III 800
5	2D 1H-1H NOESY	3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP)	90% H2O/10% D2O	50 mM	7	760 mmHg	278	Bruker AVANCE III 800
3	2D 1H-1H COSY	3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP)	90% H2O/10% D2O	50 mM	7	760 mmHg	278	Bruker AVANCE III 800
4	2D 1H-13C HSQC	3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP)	90% H2O/10% D2O	50 mM	7	760 mmHg	298	Bruker AVANCE III 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
2	Bruker	AVANCE III	800

NMR Refinement
Method	Details	Software
torsion angle dynamics		X-PLOR NIH
simulated annealing	molecular dynamics	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	Sparky		Goddard
2	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
3	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
4	peak picking	Sparky		Goddard
5	processing	TopSpin		Bruker Biospin
6	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
7	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore