5M2L | pdb_00005m2l

Structure of DNA tetrameric AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

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	1.0 mM DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride	90% H2O/10% D2O	150 mM	6	1 atm	273	Varian Uniform NMR System 800
2	1D 1H-15N HSQC	1 mM residue specific 15N and 13C DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride	90% H2O/10% D2O	150 mM	6	1 atm	273	Varian Uniform NMR System 600
3	2D 1H-15N HSQC	1 mM residue specific 15N and 13C DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride	90% H2O/10% D2O	150 mM	6	1 atm	273	Varian Uniform NMR System 800
4	2D 1H-13C HSQC	1 mM residue specific 15N and 13C DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride	90% H2O/10% D2O	150 mM	6	1 atm	273	Varian Uniform NMR System 600
5	2D 1H-1H NOESY	1 mM D8 residue specific labeled DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride	90% H2O/10% D2O	150 mM	6	1 atm	273	Varian Uniform NMR System 800
7	2D 1H-1H NOESY	1 mM uniformly labeled with D8 DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 150 mM sodium chloride	90% H2O/10% D2O	150 mM	6	1 atm	273	Varian Uniform NMR System 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	Uniform NMR System	600
2	Varian	Uniform NMR System	800

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	chemical shift assignment	Sparky		Goddard
4	peak picking	Sparky