6YFY
Solid-state NMR structure of the D-Arg4,L10-teixobactin - Lipid II complex in lipid bilayers.
SOLID-STATE NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NH | 25 mM sodium chloride, 40 mM sodium phosphate, 1.6 mM [U-99% 13C; U-99% 15N] D-Arg,Leu10-teixobactin, 0.8 mM [U-99% 13C; U-99% 15N] Lipid II, 1.6 mM [U-99% 13C; U-99% 15N] Leu10-teixobactin | 40mM Phosphate 25mM NaCl | 40 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 950 |
2 | 2D CC | 25 mM sodium chloride, 40 mM sodium phosphate, 1.6 mM [U-99% 13C; U-99% 15N] D-Arg,Leu10-teixobactin, 0.8 mM [U-99% 13C; U-99% 15N] Lipid II, 1.6 mM [U-99% 13C; U-99% 15N] Leu10-teixobactin | 40mM Phosphate 25mM NaCl | 40 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 950 |
3 | 2D TOBSY | 25 mM sodium chloride, 40 mM sodium phosphate, 1.6 mM [U-99% 13C; U-99% 15N] D-Arg,Leu10-teixobactin, 0.8 mM [U-99% 13C; U-99% 15N] Lipid II, 1.6 mM [U-99% 13C; U-99% 15N] Leu10-teixobactin | 40mM Phosphate 25mM NaCl | 40 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 950 |
4 | 3D HNCO | 25 mM sodium chloride, 40 mM sodium phosphate, 1.6 mM [U-99% 13C; U-99% 15N] D-Arg,Leu10-teixobactin, 0.8 mM [U-99% 13C; U-99% 15N] Lipid II, 1.6 mM [U-99% 13C; U-99% 15N] Leu10-teixobactin | 40mM Phosphate 25mM NaCl | 40 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 950 |
6 | 3D HNCA | 25 mM sodium chloride, 40 mM sodium phosphate, 1.6 mM [U-99% 13C; U-99% 15N] D-Arg,Leu10-teixobactin, 0.8 mM [U-99% 13C; U-99% 15N] Lipid II, 1.6 mM [U-99% 13C; U-99% 15N] Leu10-teixobactin | 40mM Phosphate 25mM NaCl | 40 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 950 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 950 |
2 | Bruker | AVANCE III | 700 |
3 | Bruker | AVANCE III | 800 |
4 | Bruker | AVANCE III | 500 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle dynamics | HADDOCK |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted |
Conformers Calculated Total Number | 26 |
Conformers Submitted Total Number | 26 |
Representative Model | 1 (medoid) |
Additional NMR Experimental Information | |
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Details | All the structures are aligned to chains A,B,E,F of model 5. Residues 1-5 and 9-12 in chains C,D,G,H are highly flexible (no NMR restraints were applied).Alignment was performed in PyMol using the alignto command, and we converted the pdb file to a cif file using the online convertor provided by wwPDB. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | CNS | Brunger A. T. et.al. | |
2 | structure calculation | HADDOCK | Bonvin | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | TopSpin | Bruker Biospin |