1ED0 | pdb_00001ed0

NMR structural determination of viscotoxin A3 from Viscum album L.

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	2mM Viscotoxin A3 1H; 50mM H3PO4/NaOH aqueous buffer; 90% H2O, 10% D2O	90% H2O/10% D2O	50mM	3.6	ambient	285
2	DQF-COSY	2mM Viscotoxin A3 1H; 50mM H3PO4/NaOH aqueous buffer; 90% H2O, 10% D2O	90% H2O/10% D2O	50mM	3.6	ambient	285
3	TOCSY	2mM Viscotoxin A3 1H; 50mM H3PO4/NaOH aqueous buffer; 90% H2O, 10% D2O	90% H2O/10% D2O	50mM	3.6	ambient	285
4	2D NOESY	2mM Viscotoxin A3 1H; 50mM H3PO4/NaOH aqueous buffer; 100% D2O	100% D2O	50mM	3.6	ambient	285
5	DQF-COSY	2mM Viscotoxin A3 1H; 50mM H3PO4/NaOH aqueous buffer; 100% D2O	100% D2O	50mM	3.6	ambient	285
6	TOCSY	2mM Viscotoxin A3 1H; 50mM H3PO4/NaOH aqueous buffer; 100% D2O	100% D2O	50mM	3.6	ambient	285

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	500

NMR Refinement
Method	Details	Software
RESTRAINED SIMULATED ANNEALING IN TORSION ANGLE SPACE, ITERATIVE RESTRAINTS REFINEMENT, RESTRAINED MOLECULAR DYNAMICS IN CARTESIAN COORDINATE SPACE MINIMIZATION	1010 distance restraints were calculated reduced to 734 (230 intraresidue, 172 sequential, 191 medium range, 141 long range) after removal of irrelevant restraints. Calculation started with 200 randomized conformers and consistently violated restraints were checked and relaxed where necessary. This procedure was repeated until no consistent violations were found in half or more of the structures. 600 new calculations were started and the 20 structures with lowest target function were analyzed. The structure with lowest target function and the structure exhibiting the largest RMSD with it were subjected to restrained molecular dynamics (20 cycles of 15 ps restrained molecular dynamics followed by minimization). All even structures from the last 10 minimized structures were retained from both sets and deposited.	DYANA

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	600
Conformers Submitted Total Number	10
Representative Model	8 (lowest average rmsd with other structures in the ensemble)

Additional NMR Experimental Information
Details	This structure was determined using standard 2D homonuclear techniques

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	DYANA	1.4	Guentert, Wuethrich
2	refinement	Discover	98	MSI
3	collection	XwinNMR	1.2	Bruker Spectrospin
4	data analysis	XEASY	1.2	Eccles, Xia, Bartels, Guentert, Billeter, Wuethrich