1D0T
SOLUTION STRUCTURE OF A PHOSPHOROTHIOATE MODIFIED RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2.0 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 EDTA | 90% H2O/10% D2O | ~50mM | 6.8 | ambient | 298 | |
2 | 3D_15N-separated_NOESY | 2.0 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 EDTA | 90% H2O/10% D2O | ~50mM | 6.8 | ambient | 298 | |
3 | 3D_15N-separated_NOESY | 2.0 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 EDTA | 100% D2O | |||||
4 | DQF-COSY | 2.0 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 EDTA | 100% D2O | |||||
5 | 31P-1H HetCor | 2.0 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 EDTA | 100% D2O | |||||
6 | 2D 13C-filtered NOESY | 2.0 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 EDTA | 100% D2O |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 500 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing and molecular dynamics refinement | structures 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 | |
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Conformer Selection Criteria | back 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 Number | 30 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | The 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 | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | UXNMR | 1994 | Spectraspin |
2 | processing | Felix | 1998 | Biosym-MSI |
3 | structure solution | X-PLOR | 3.851 | Brunger |
4 | refinement | X-PLOR | 3.851 | Brunger |