2RP3
Solution Structure of Cyanovirin-N Domain B Mutant
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 1.5mM [U-100% 15N] CVNmutDB, 1.5mM [U-100% 13C; U-100% 15N] CVNmutDB | 90% H2O/10% D2O | 6.0 | atm | 303 | ||
2 | 3D CBCA(CO)NH | 1.5mM [U-100% 15N] CVNmutDB, 1.5mM [U-100% 13C; U-100% 15N] CVNmutDB | 90% H2O/10% D2O | 6.0 | atm | 303 | ||
3 | 3D HNCACB | 1.5mM [U-100% 15N] CVNmutDB, 1.5mM [U-100% 13C; U-100% 15N] CVNmutDB | 90% H2O/10% D2O | 6.0 | atm | 303 | ||
4 | 3D HCCH-TOCSY | 1.5mM [U-100% 15N] CVNmutDB, 1.5mM [U-100% 13C; U-100% 15N] CVNmutDB | 90% H2O/10% D2O | 6.0 | atm | 303 | ||
5 | 3D 15N-NOESY HSQC | 1.5mM [U-100% 15N] CVNmutDB, 1.5mM [U-100% 13C; U-100% 15N] CVNmutDB | 90% H2O/10% D2O | 6.0 | atm | 303 | ||
6 | 13C-NOESY | 1.5mM [U-100% 15N] CVNmutDB, 1.5mM [U-100% 13C; U-100% 15N] CVNmutDB | 90% H2O/10% D2O | 6.0 | atm | 303 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | BACKBONE NH DIPOLAR COUPLINGS, RMS=0.64HZ | CYANA |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
---|---|
Details | THE INITIAL STRUCTURES WERE OBTAINED USING CYANA AUTOMATIC CALCULATION, BASED ON CHEMICAL SHIFT LISTS FROM SEQUENCE-SPECIFIC RESONANCE ASSIGNMENT AND NOES FROM 15N AND 13C-EDITED 3D-NOESY SPECTRA. THROUGHOUT ALL CALCULATIONS, 126 BACKBONE TORSION ANGLE CONSTRAINTS DERIVED FROM TALOS, WERE EMPLOYED. CNS WAS USED FOR FURTHER REFINEMENT, USING THE DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS OBTAINED FROM THE FINAL CYCLE OF THE CYANA CALCULATION, AND SEVERAL ADDITIONAL NOE CONSTRAINTS FROM MANUAL CHECKING OF THE 3D NOESY DATA. IN TOTAL, 2076 EXPERIMENTAL NOE-RESTRAINTS (~20 PER RESIDUE) WERE EMPLOYED. FROM NOE-DERIVED ENSEMBLE OF 50 STRUCTURES THE 20 LOWEST ENERGY STRUCTURES WERE FURTHER REFINED AGAINST 15N-1H RESIDUAL DIPOLAR COUPLINGS (62) WITH THE PROGRAM DYNAMO INCLUDED IN THE NMRPIPE PACKAGE. |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | CYANA | HERRMANN, GUNTERT, WUTHRICH | |
2 | refinement | CNS | BRUNGER, ADAMS, CLORE, DELANO, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARREN | |
3 | structure solution | TopSpin | Bruker Biospin | |
4 | structure solution | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
5 | structure solution | NMRView | Johnson, One Moon Scientific | |
6 | structure solution | CYANA | Guntert, Mumenthaler and Wuthrich | |
7 | structure solution | TALOS | Cornilescu, Delaglio and Bax | |
8 | structure solution | DYNAMO(NMRpipe) | Cornilescu, Delaglio and Bax |