1D1D
NMR SOLUTION STRUCTURE OF THE CAPSID PROTEIN FROM ROUS SARCOMA VIRUS
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 4D_13C-SEPARATED_NOESY | ~1 MM CA_RSV, 10 MM PHOSPHATE (PH 6.0), 0.2 MM N3NA, 0.1 MM EDTA, 0.1 MM PMSF, 1 MG/L PEPSTATIN A, 5 MM BETA-MERCAPTOETHANOL | 90% H2O/10% D2O | 10 mM PHOSPHATE | 6.00 | 1 atm | 303.00 | |
| 2 | 4D_13C/15N-SEPARATED_ NOESY | ~1 MM CA_RSV, 10 MM PHOSPHATE (PH 6.0), 0.2 MM N3NA, 0.1 MM EDTA, 0.1 MM PMSF, 1 MG/L PEPSTATIN A, 5 MM BETA-MERCAPTOETHANOL | 90% H2O/10% D2O | 10 mM PHOSPHATE | 6.00 | 1 atm | 303.00 | |
| 3 | 4D_15N-SEPARATED_ NOESY | ~1 MM CA_RSV, 10 MM PHOSPHATE (PH 6.0), 0.2 MM N3NA, 0.1 MM EDTA, 0.1 MM PMSF, 1 MG/L PEPSTATIN A, 5 MM BETA-MERCAPTOETHANOL | 90% H2O/10% D2O | 10 mM PHOSPHATE | 6.00 | 1 atm | 303.00 | |
| 4 | 3D_15N- SEPARATED_NOESY | ~1 MM CA_RSV, 10 MM PHOSPHATE (PH 6.0), 0.2 MM N3NA, 0.1 MM EDTA, 0.1 MM PMSF, 1 MG/L PEPSTATIN A, 5 MM BETA-MERCAPTOETHANOL | 90% H2O/10% D2O | 10 mM PHOSPHATE | 6.00 | 1 atm | 303.00 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| TORSION ANGLE DYNAMICS SIMULATED ANNEALING | 20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD TORSION ANGLE SIMULATED ANHEALING PROTOCOL. PRELIMINARY CALCULATIONS WERE CARRIED OUT INDEPENDENTLY FOR EACH OF THE TWO N- AND C- TERMINAL DOMAINS OF THE PROTEIN. INITIALLY ONLY NOE DISTANCE CONSTRAINTS WERE IMPOSED. THE INITIAL STRUCTURES WERE THEN USED TO ASSES THE ACCURACY OF THE TORSION ANGLE CONSTRAINTS GENERATED BY ANALYSIS OF HA, CA, CB, CO AND N CHEMICAL SHIFTS WITH THE PROGRAM TALOS. FINALLY, UPPER AND LOWER LIMIT DISTANCE CONSTRAINTS WERE IMPOSED FOR UNAMBIGUOUS INTRAHELICAL H-BONDS. | DYANA |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 20 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 7 (n/a) |
| Additional NMR Experimental Information | |
|---|---|
| Details | THE 1H, 13C, AND 15N CHEMICAL SHIFT ASSIGNMENTS HAVE BEEN DEPOSITED ATTHE BIOMOLECULAR RESONANCE DATABANK (BMRB ENTRY 4384). |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | DYANA | 1.5 | P.GUNTHER, ETH-ZURICH |
| 2 | structure solution | XwinNMR | 2.5 | |
| 3 | structure solution | NMRPipe | 1999 | |
| 4 | structure solution | NMRView | 3.0 | |
| 5 | structure solution | TALOS | 1999.019.15.47 | |
