2KEK
Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O3
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D 1H-13C NOESY | 0.7 mM DNA (5'-strand1-3'), 0.7 mM DNA (5'-strand2-3'), 0.7 mM Lac headpiece dimer, 5% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 5% U-100% 2H d8-glycerol, 0.01% sodium azide | 95% H2O/5% D2O | 0.03 | 6 | ambient | 315 | |
2 | 3D 1H-15N NOESY | 0.7 mM DNA (5'-strand1-3'), 0.7 mM DNA (5'-strand2-3'), 0.7 mM Lac headpiece dimer, 5% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 5% U-100% 2H d8-glycerol, 0.01% sodium azide | 95% H2O/5% D2O | 0.03 | 6 | ambient | 315 | |
3 | 2D 1H-1H NOESY | 0.7 mM DNA (5'-strand1-3'), 0.7 mM DNA (5'-strand2-3'), 0.7 mM Lac headpiece dimer, 5% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 5% U-100% 2H d8-glycerol, 0.01% sodium azide | 95% H2O/5% D2O | 0.03 | 6 | ambient | 315 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 750 |
2 | Bruker | AVANCE | 600 |
3 | Bruker | AVANCE | 900 |
4 | Bruker | AVANCE | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | CNS |
NMR Ensemble Information | |
---|---|
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 | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
2 | chemical shift assignment | XwinNMR | Bruker Biospin | |
3 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | refinement | HADDOCK | 2.1 | Dominguez, Boelens, Bonvin |