7L55
Solution NMR structure of the cyclic plant protein PDP-23 in DPC micelles
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 1D | 2 mg/mL PDP-23, 12 mM DPC | 90% H2O/10% D2O | 0 mM | 5 | ambient | 298 | Bruker AVANCE III 700 |
2 | 2D 1H-1H TOCSY | 2 mg/mL PDP-23, 12 mM DPC | 90% H2O/10% D2O | 0 mM | 5 | ambient | 298 | Bruker AVANCE III 700 |
3 | 2D 1H-1H NOESY | 2 mg/mL PDP-23, 12 mM DPC | 90% H2O/10% D2O | 0 mM | 5 | ambient | 298 | Bruker AVANCE III 700 |
4 | 2D 1H-13C HSQC | 2 mg/mL PDP-23, 12 mM DPC | 90% H2O/10% D2O | 0 mM | 5 | ambient | 298 | Bruker AVANCE III 700 |
5 | 2D 1H-1H TOCSY | 2 mg/mL PDP-23, 12 mM DPC | 90% H2O/10% D2O | 0 mM | 5 | ambient | 288 | Bruker AVANCE III 700 |
6 | 2D 1H-1H TOCSY | 2 mg/mL PDP-23, 12 mM DPC | 90% H2O/10% D2O | 0 mM | 5 | ambient | 293 | Bruker AVANCE III 700 |
8 | 2D 1H-1H TOCSY | 2 mg/mL PDP-23, 12 mM DPC | 90% H2O/10% D2O | 0 mM | 5 | ambient | 303 | Bruker AVANCE III 700 |
7 | 2D 1H-1H TOCSY | 2 mg/mL PDP-23, 12 mM DPC | 90% H2O/10% D2O | 0 mM | 5 | ambient | 308 | Bruker AVANCE III 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 700 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Simulated annealing using torsion angle dynamics | CYANA |
simulated annealing | Refinement in explicit water using Cartesian space | CNS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with acceptable covalent geometry, structures with lowest energy |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | TopSpin | Bruker Biospin | |
2 | processing | TopSpin | Bruker Biospin | |
3 | chemical shift assignment | CARA | Keller and Wuthrich | |
4 | peak picking | CARA | Keller and Wuthrich | |
5 | structure calculation | CYANA | Guntert, Mumenthaler and Wuthrich | |
6 | structure calculation | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
7 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read |