2N9R | pdb_00002n9r

Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics

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	5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate	90% H2O/10% D2O		7	ambient	298
2	2D 1H-1H NOESY	5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate	90% H2O/10% D2O		7	ambient	298
3	2D 1H-13C HSQC	5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate	90% H2O/10% D2O		7	ambient	298
4	2D 1H-15N sfHMQC	5 % TSP, 10 % D2O, 90 % H2O, 100 mM SDS, 30 mM sodium phosphate	90% H2O/10% D2O		7	ambient	298

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

NMR Refinement
Method	Details	Software
simulated annealing	In the final step was performed refinement in water	X-PLOR NIH

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	X-PLOR NIH	2.28	Schwieters, Kuszewski, Tjandra and Clore
2	refinement	X-PLOR NIH	2.28	Schwieters, Kuszewski, Tjandra and Clore
3	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	data analysis	NMRView		Johnson, One Moon Scientific
6	geometry optimization	TALOS		Cornilescu, Delaglio and Bax
7	data analysis	TALOS		Cornilescu, Delaglio and Bax
8	data analysis	QUEEN		Nabuurs, Spronk, Krieger, Maassen, Vriend and Vuister
9	data analysis	ProcheckNMR		Laskowski and MacArthur
10	data analysis	MOLMOL		Koradi, Billeter and Wuthrich