SOLUTION STRUCTURE AND BASE PERTURBATION STUDIES REVEAL A NOVEL MODE OF ALKYLATED BASE RECOGNITION BY 3-METHYLADENINE DNA GLYCOSYLASE I
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_13C-separated_NOESY | 0.5-1mM 13C, 15N, 75% 2H labeled3-methyladenine DNA glycosylase I, 100mM Nacl, 3mM DTT, 0.34mM NaN3, 10mM phosphate buffer, pH6.6 ~8, fold ( or 13C8 labeled) 3-methyladenine | H20 | 10mM phosphate buffer | 6.6 | ambient | 293 | |
| 2 | 3D_15N-separated_NOESY | 0.5-1mM 13C, 15N, 75% 2H labeled3-methyladenine DNA glycosylase I, 100mM Nacl, 3mM DTT, 0.34mM NaN3, 10mM phosphate buffer, pH6.6 ~8, fold ( or 13C8 labeled) 3-methyladenine | H20 | |||||
| 3 | 2D NOESY | 0.5-1mM 13C, 15N, 75% 2H labeled3-methyladenine DNA glycosylase I, 100mM Nacl, 3mM DTT, 0.34mM NaN3, 10mM phosphate buffer, pH6.6 ~8, fold ( or 13C8 labeled) 3-methyladenine | H20 | |||||
| 4 | 13C-edited HSQC | 0.5-1mM 13C, 15N, 75% 2H labeled3-methyladenine DNA glycosylase I, 100mM Nacl, 3mM DTT, 0.34mM NaN3, 10mM phosphate buffer, pH6.6 ~8, fold ( or 13C8 labeled) 3-methyladenine | H20 | |||||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 500 |
| 2 | Bruker | DMX | 600 |
| 3 | Varian | UNITYPLUS | 500 |
| 4 | Varian | INOVA | 600 |
| 5 | Bruker | DMX | 750 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics | the structures are based on a total of 2494 restraints, 2140 are NOE-derived distance constraints, 222 dihedral angle restraints, 132 h-bond constraints | CNS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 25 |
| Representative Model | 8 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | 1H-13C HMQC |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | CNS | 1.1 | Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L. |
| 2 | refinement | X-PLOR | NIH-2.0.2 | Clore, G.M., Kuszewski, J. |
| 3 | data analysis | Sparky | 3.93 | Goddard, T.D., Kneller, D.G. |
| 4 | processing | NMRPipe | NIH | Delaglio, F. |
