SOLUTION NMR

NMR Experiment
Experiment Type Sample Contents Ionic Strength Solvent pH Pressure Temprature (K)
1 3D SEQUENTIAL ASSIGNMENT PROTOCOL 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O ? 90% H2O/10% D2O 6.8 AMBIENT 310
2 3D HNHA 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O ? 90% H2O/10% D2O 6.8 AMBIENT 310
3 4D_13C-SEPARATED_NOESY 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O ? 90% H2O/10% D2O 6.8 AMBIENT 310
4 4D_13C/15N-SEPARATED_NOESY 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O ? 90% H2O/10% D2O 6.8 AMBIENT 310
5 3D_15N-SEPARATED_NOESY 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O ? 90% H2O/10% D2O 6.8 AMBIENT 310
6 3D_13C_SEPARATED_NOESY, 2D NOESY 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O ? 90% H2O/10% D2O 6.8 AMBIENT 310
7 2D TOCSY AND 2D COSY 1-2mM PhoB-DNA U-15N, 13C; 10mM potassium phosphate buffer; 90% H2O, 10% D2O ? 90% H2O/10% D2O 6.8 AMBIENT 310
NMR Spectrometer Information
Spectrometer Manufacturer Model Field Strength
NMR Refinement
Method Details Software
simulated annealing molecluar dynamics THE STRUCTURES ARE BASED ON A TOTAL OF 2508 RESTRAINTS, 2263 ARE NOE-DERIVED DISTANCE RESTRAINTS 229 ARE DIHEDRAL ANGLE RESTRAINTS AND 16 ARE RESTRAINTS OF DNA BASE PLANALITY RESTRAINTS. STRUCTURE CALCULATIONS WERE PERFORMED WITH CNS BY FOLLOWIN PROCEDURE. FIRST, ONLY THE STRUCTURES OF PROTEIN WERE CALCULATED USING THE HYBRID DISTANCE GEOMETRY-SIMULATED ANNEAING PROTOCOL WITH THE INTRA-PROTEIN RESTRAINTS, 10 OUT OF 100 CALCULATED STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATION GREATER THAN 0.2 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATION GREATER THAN 2 DEGREES and A LOW TARGET ENERGY. SECOND, THE PROTEIN AND AN IDEALIZED B-FORM OF 16-MER DUPLEX DNA WERE DOCKED BY A SIMULATED ANNEALING PROTOCOL, FOR WHICH THE INTRA-DNA, INTER-MOLECULAR AND INTRA-PROTEIN RESTRAINTS WERE EMPLOYED. AS AN INITIAL STRUCTURE, EACH OF THE 10 PROTEIN STRUCTURES WAS PLACED IN 15 DIFFERENT POSITIONS 50 ANGSTROMS AWAY FROM THE DNA. NEXT, EACH OF THE 150 DOCKED COMPLEX STRUCTURES WAS FURTHER REFINED BY A SIMULATED ANNEALING PROTOCOL. FINALLY, 20 STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATION GREATER THAN 0.2 ANGSTROME AND NO TORSION ANGLE VIOLATION THAN 2 DEGREES AND A LOW TARGET ENERGY. ADDITIONALLY, 10 CNS-SELECTED STRUCTURES WERE REFINED IN REALISTIC SOLUTION SISTEM BY USING MOLECULAR DYNAMICS SIMULATION PROGRAM, MARBLE WITH RESTRAINT FUNCTIONS FOR NOE DISTANCE DIHEDRAL ANGLE AND PLANARITY OF DNA BASE PAIR USED IN CNS. 1
NMR Ensemble Information
Conformer Selection Criteria structures with the least restraint violations, structures with the lowest energy
Conformers Calculated Total Number 100
Conformers Submitted Total Number 10
Representative Model 1 (closest to the average)
Computation: NMR Software
# Classification Version Software Name Author
1 data analysis ? NMRPipe ?
2 data analysis ? PIPP ?
3 refinement 1.0 CNS A.BRUNGER et al.
4 refinement 0.3.46 MARBLE M.Ikeguchi