8QRX
Solution NMR structure of the peptidyl carrier domain TomAPCP from the Tomaymycin non-ribosomal peptide synthetase in its substrate-loaded state
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 | 350 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O | 90% H2O/10% D2O | 265 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 600 |
2 | 2D 1H-13C HSQC | 100 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O | 90% H2O/10% D2O | 265 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III HD 850 |
3 | 2D 1H-13C HSQC | 500 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 % w/v sodium azide, 100 v/v [U-2H] D2O | 100% D2O | 265 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III HD 850 |
4 | 3D 1H-15N NOESY | 350 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O | 90% H2O/10% D2O | 265 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 600 |
5 | 3D 1H-13C NOESY | 500 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 % w/v sodium azide, 100 v/v [U-2H] D2O | 100% D2O | 265 mM | 7.0 | 1 atm | 298 | Bruker AVANCE III HD 850 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 600 |
2 | Bruker | AVANCE III HD | 850 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | CNS | |
torsion angle dynamics | CNS | |
molecular dynamics | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 3.2 | Bruker Biospin |
2 | processing | NMRPipe | 10.2 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
3 | peak picking | CcpNmr Analysis | 2.4 | CCPN |
4 | chemical shift assignment | CcpNmr Analysis | 2.4 | CCPN |
5 | data analysis | CcpNmr Analysis | 2.4 | CCPN |
6 | structure calculation | ARIA | 2.3 | Linge, O'Donoghue and Nilges |
7 | structure calculation | CNS | 1.21 | Brunger, Adams, Clore, Gros, Nilges and Read |
8 | structure calculation | CNS | 1.21 | Brunger, Adams, Clore, Gros, Nilges and Read |
9 | structure calculation | CNS | 1.21 | Brunger, Adams, Clore, Gros, Nilges and Read |