1ZQ3
NMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCC
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_13C-separated_NOESY | 1mM Bicoid Homeodomain (15N/13C), 1mM Duplex DNA (unlabeled), 10mM phosphate buffer, pH 7.0, 1mM DTT, 1mM PMSF, 1mM EDTA, 1mM sodium azide, 0.3mM leupeptin, 0.2mM pefabloc (Roche), 90% H2O, 10% D2O | 90% H2O/10% D2O | 7.0 | 1 atm | 295 | ||
2 | 3D_15N-separated_NOESY | 1mM Bicoid Homeodomain (15N/13C), 1mM Duplex DNA (unlabeled), 10mM phosphate buffer, pH 7.0, 1mM DTT, 1mM PMSF, 1mM EDTA, 1mM sodium azide, 0.3mM leupeptin, 0.2mM pefabloc (Roche), 90% H2O, 10% D2O | 90% H2O/10% D2O | 7.0 | 1 atm | 295 | ||
3 | HNHA | 1mM Bicoid Homeodomain (15N/13C), 1mM Duplex DNA (unlabeled), 10mM phosphate buffer, pH 7.0, 1mM DTT, 1mM PMSF, 1mM EDTA, 1mM sodium azide, 0.3mM leupeptin, 0.2mM pefabloc (Roche), 90% H2O, 10% D2O | 90% H2O/10% D2O | 7.0 | 1 atm | 295 | ||
4 | 2D NOESY | 1mM Bicoid Homeodomain (15N/13C), 1mM Duplex DNA (unlabeled), 10mM phosphate buffer, pH 7.0, 1mM DTT, 1mM PMSF, 1mM EDTA, 1mM sodium azide, 0.3mM leupeptin, 0.2mM pefabloc (Roche), 90% H2O, 10% D2O | 90% H2O/10% D2O | 7.0 | 1 atm | 295 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | INOVA | 800 |
NMR Refinement | ||
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Method | Details | Software |
protein structure - fast torsion angle dynamics algorithm (CYANA2.0), DNA structure - NUCGEN and simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex - simulated annealing with NMR-derived energy restraints (AMBER7.0), protein-DNA complex refinement - explicit solvent MD simulations (AMBER7.0) | 1724 total restraints used, 1076 protein distance restraints(NOESY), 34 protein hydrogen bond restraints(3D NOESY ,i-i+4), 134 angle restraints(HNHA), 192 DNA distance restraints(2D NOESY), 55 watson-crick restraints(B-DNA), 200 DNA angle restraints(B-DNA), 33 protein-DNA distance restraints (2D NOESY) | CYANA |
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 | 3 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | CYANA | 2.0 | Peter Guntert |
2 | refinement | Amber | 7.0 | D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, B. Wang, D.A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J.W. Caldwell, W.S. Ross, and P.A. Kollman. |
3 | data analysis | Sparky | 3.109 | T. D. Goddard and D. G. Kneller |
4 | processing | NMRPipe | F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax |