2C06
NMR-based model of the complex of the toxin Kid and a 5-nucleotide substrate RNA fragment (AUACA)
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 1H-15N HSQC | 95% D2O / 5% WATER | 100 mM | 5.8 | 1.0 atm | 303.0 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 750 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| HADDOCK | STRUCTURE OF THE COMPLEX WAS CALCULATED WITH HADDOCK FOLLOWING STANDARD PROTOCOLS DOMINGUEZ, BOELENS AND BONVIN, JACS 2003, 125, 1731-1737 | CNS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | LOWEST 10 ENERGY STRUCTURES IN LOWEST ENERGY CLUSTER |
| Conformers Calculated Total Number | 200 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (n/a) |
| Additional NMR Experimental Information | |
|---|---|
| Details | THE STRUCTURE OF THE COMPLEX WAS DETERMINED WITH HADDOCK USING 28 AMBIGUOUS INTERACTION RESTRAINTS DERIVED FROM NMR CHEMICAL SHIFT PERTURBATION DATA, MUTAGENESIS DATA AND KNOWN RNA CLEAVAGE MECHANISM, USING THE CRYSTAL STRUCTURE OF THE KID DIMER (PDB ENTRY 1M1F) AS STARTING POINT. THE CHEMICAL SHIFT PERTURBATION DATA WERE OBTAINED BY ANALYSIS OF 1H-15N HSQC SPECTRA RECORDED WITH INCREASING RNA CONCENTRATIONS. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | CNS | BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARREN | |
| 2 | structure solution | NMRView | ||
| 3 | structure solution | CNS | ||
| 4 | structure solution | HADDOCK | ||
