8S2A | pdb_00008s2a

NMR structure of xantholysin A in micellar DPC solution

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	3.2 mM xantholysin A, 162.9 mM [U-2H] DPC	90% H2O/10% D2O	26 (buffer only) mM	7.4	1 atm	298	Bruker AVANCE II 700
2	2D 1H-1H TOCSY	3.2 mM xantholysin A, 162.9 mM [U-2H] DPC	90% H2O/10% D2O	26 (buffer only) mM	7.4	1 atm	298	Bruker AVANCE II 700
3	2D 1H-1H COSY	3.2 mM xantholysin A, 162.9 mM [U-2H] DPC	90% H2O/10% D2O	26 (buffer only) mM	7.4	1 atm	298	Bruker AVANCE II 700
4	2D 1H-13C HSQC	3.2 mM xantholysin A, 162.9 mM [U-2H] DPC	90% H2O/10% D2O	26 (buffer only) mM	7.4	1 atm	298	Bruker AVANCE II 700

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE II	700

NMR Refinement
Method	Details	Software
molecular dynamics	The lowest energy NMR structure issued from CNS was refined using unrestrained AMBER molecular dynamics simulations (against the ff14SB force field). Here, we modelled the interaction of a single peptide molecule with an explicit dodecylphosphocholine (DPC) micelle. The representative peptide conformation of the trajectory (=refined structure) was selected using cluster analysis. Solvent model: TIP3P. Occasional too-close contacts present in the NMR structure ensemble (structures #2-#11) are fully removed during the AMBER moleculary dynamics refinement (structure #1)	Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	11
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	data analysis	AmberTools		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	processing	TopSpin	3.x	Bruker Biospin
4	collection	TopSpin	3.x	Bruker Biospin
5	peak picking	CcpNmr Analysis		Vuister et al.
6	structure calculation	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
8	chemical shift assignment	CcpNmr Analysis		Vuister et al.