1D0T

SOLUTION STRUCTURE OF A PHOSPHOROTHIOATE MODIFIED RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA90% H2O/10% D2O~50mM6.8ambient298
23D_15N-separated_NOESY2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA90% H2O/10% D2O~50mM6.8ambient298
33D_15N-separated_NOESY2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA100% D2O
4DQF-COSY2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA100% D2O
531P-1H HetCor2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA100% D2O
62D 13C-filtered NOESY2.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA100% D2O
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAMX500
NMR Refinement
MethodDetailsSoftware
simulated annealing and molecular dynamics refinementstructures were calculated using 313 conformationally restrictive NOE distance constraints (i.e., intra-residue sugar-sugar NOEs are not included), 20 H-bond base pair constraints, 30 backbone dihedral restraints, and dihedral restraints to restrict sugar pucker conformation. Parameter file was modified to incorporate bond-length, bond-angle, charge, van der Waal's radius for the Rp phosphoryl sulfur atoms located 5' to each adenine in the sequence. [Jaroszewski, JW., et al., Anti-Cancer Drug Design ( 1992) 7, 253; Florian, J. et al., J. Am. Chem. Soc. (1998) 120, 7959].UXNMR
NMR Ensemble Information
Conformer Selection Criteriaback calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations, structures with the lowest energy
Conformers Calculated Total Number30
Conformers Submitted Total Number10
Representative Model1 (minimized average structure)
Additional NMR Experimental Information
DetailsThe structure was determined using standard 2D homonuclear and 2D/3D heteronuclear techniques. Filtered experiments used to identify inter-residue NOEs involving unlabeled A residues
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionUXNMR1994Spectraspin
2processingFelix1998Biosym-MSI
3structure solutionX-PLOR3.851Brunger
4refinementX-PLOR3.851Brunger