6MI9
The peptide PaAMP1B3 is an analog derived from the PaAMP1. The sequence of the ribosomal protein of Pyrobaculum aerophylum was used as template for rational design, using the Joker algorithm.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H TOCSY | 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O | 90% H2O/10% D2O | acid | 4.3 | 1 atm | 298 | Bruker AVANCE III 500 |
2 | 2D 1H-1H NOESY | 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O | 90% H2O/10% D2O | acid | 4.3 | 1 atm | 298 | Bruker AVANCE III 500 |
3 | 2D 1H-13C HSQC | 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O | 90% H2O/10% D2O | acid | 4.3 | 1 atm | 298 | Bruker AVANCE III 500 |
4 | 2D 1H-15N HMQC | 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O | 90% H2O/10% D2O | acid | 4.3 | 1 atm | 298 | Bruker AVANCE III 500 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 500 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | X-PLOR NIH |
NMR Ensemble Information | |
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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 | ||||
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# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
2 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
3 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
6 | geometry optimization | TALOS | Cornilescu, Delaglio and Bax |