2MAV
NMR Structure of N2-IQ-dG at the G3 position in the NarI recognition sequence
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.560 uM DNA (5'-D(*CP*TP*CP*GP*GP*CP*IQGP*CP*CP*AP*TP*C)-3'), 0.560 uM DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'), 0.560 uM N2-2-amino-3-methylimidazo[4,5-f]quinoline-deoxyguanosine | 100% D2O | 0.1 | 7 | ambient | 288 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, molecular dynamics | TopSpin | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
| Conformers Calculated Total Number | 10 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | TopSpin | 3.2 | Bruker Biospin |
| 2 | collection | TopSpin | 3.2 | Bruker Biospin |
| 3 | chemical shift assignment | Sparky | 3.115 | Goddard |
| 4 | data analysis | Sparky | 3.115 | Goddard |
| 5 | peak picking | Sparky | 3.115 | Goddard |
| 6 | structure solution | Amber | 10 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 7 | refinement | Amber | 10 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 8 | refinement | CORMA | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
| 9 | data analysis | MARDIGRAS | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
