2N9R
Novel antimicrobial peptide PaDBS1R1 designed from the ribosomal protein L39E from Pyrobaculum aerophilum using bioinformatics
SOLUTION NMR
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 |