2N2L
NMR structure of yersinia pestis ail (attachment invasion locus) in decylphosphocholine micelles calculated with implicit membrane solvation
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.4-0.5 mM [U-100% 13C; U-100% 15N] Yersinia pestis Ail, 20 mM sodium phosphate, 5 mM sodium chloride, 170 mM decyl-phosphocholine (DePC) | 90% H2O/10% D2O | 25 | 6.8 | ambient | 318 | |
2 | 3D HNCA | 0.4-0.5 mM [U-100% 13C; U-100% 15N] Yersinia pestis Ail, 20 mM sodium phosphate, 5 mM sodium chloride, 170 mM decyl-phosphocholine (DePC) | 90% H2O/10% D2O | 25 | 6.8 | ambient | 318 | |
3 | 3D HNCACB | 0.4-0.5 mM [U-100% 13C; U-100% 15N] Yersinia pestis Ail, 20 mM sodium phosphate, 5 mM sodium chloride, 170 mM decyl-phosphocholine (DePC) | 90% H2O/10% D2O | 25 | 6.8 | ambient | 318 | |
4 | 3D 1H-15N NOESY | 0.4-0.5 mM [U-100% 13C; U-100% 15N] Yersinia pestis Ail, 20 mM sodium phosphate, 5 mM sodium chloride, 170 mM decyl-phosphocholine (DePC) | 90% H2O/10% D2O | 25 | 6.8 | ambient | 318 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Structures were folded and refined using the eefxPot potential for implicit membrane solvation | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
2 | chemical shift assignment | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | chemical shift calculation | TALOS | Cornilescu, Delaglio and Bax | |
5 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
6 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |