2GLO
Solution structure of the Brinker DNA binding domain in complex with the omb enhancer
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_15N-separated_NOESY | 1mM brkDBD U-15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O | 95% H2O/5% D2O | 10mM NaCl | 5.8 | ambient | 298 | |
2 | 3D_13C-separated_NOESY | 1mM brkDBD U-13C/15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O | 95% H2O/5% D2O | 10mM NaCl | 5.8 | ambient | 298 | |
3 | 3D_dq-HNHA | 1mM brkDBD U-15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O | 95% H2O/5% D2O | 10mM NaCl | 5.8 | ambient | 298 | |
4 | 3D_dq-HAHB, 2D_HNCG, 2D_HN(CO)CG | 1mM brkDBD U-13C/15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O | 95% H2O/5% D2O | 10mM NaCl | 5.8 | ambient | 298 | |
5 | 2D_13C-selected/12C,14N-selected NOESY | 1mM brkDBD U-13C/15N, 1mM DNA omb12T5 NA; 10mM NaCl; 5mM potassium phosphate; 5mM TCEP; 0.02% NaN3; 95% H2O, 5% D2O | 95% H2O/5% D2O | 10mM NaCl | 5.8 | ambient | 298 | |
6 | DSSE, J-modulated-13C-HSQC | 0.35mM brkDBD U-13C/15N, 0.35mM DNA omb12 NA; 10mM NaCl; 20mM potassium phosphate; 2mM DTT; 0.02% NaN3; 25mg/ml Pf1-phages; 95% H2O, 5% D2O | 95% H2O/5% D2O | 10mM NaCl | 5.8 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
2 | Bruker | DRX | 800 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle dynamics; distance geometry | The structures are based on 1279 NOE-derived distance constraints, 21 Ambiguous Interaction Restraints, 21 distance restraints from hydrogen bonds, 92 RDC restraints, 30 dihedral angle restraints, 56 J-coupling constant restraints. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D and 3D heteronuclear techniques and 12C/14N-filtered-NOESY experiments for DNA assignment and intermolecular NOE contacts |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 2.6 | Bruker |
2 | processing | NMRPipe | 2.2 | Delaglio |
3 | data analysis | PIPP | 4.3.2 | Garrett |
4 | refinement | HADDOCK | 1.2 | Bonvin |