1NGO
NMR Structure of Putative 3' Terminator for B. Anthracis pagA Gene Coding Strand
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2mM 110C DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl; | 90% H2O/10% D2O | 150mM NaCl | 6.5 | ambient | 278 | |
2 | 2D NOESY | 2mM 110C DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl; | 100% D2O | 150mM NaCl | 6.5 | ambient | 298 | |
3 | 2D TOCSY | 2mM 110C DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl; | 100% D2O | 150mM NaCl | 6.5 | ambient | 298 | |
4 | DQF-COSY | 2mM 110C DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl; | 100% D2O | 150mM NaCl | 6.5 | ambient | 298 | |
5 | HMQC | 1mM 110C DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl; , 13C8 and 15N6 and 15N9 of A12 and A15 | 100% D2O | 150mM NaCl | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 500 |
NMR Refinement | ||
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Method | Details | Software |
minimization molecular dynamics | Structure is derived from 191 NOES of which, 25 involve exchangeable protons in the stem, 153 NOEs involve non-exchangeable protons in the stem, 13 NOEs involve non-exchangeable protons in the loop, 50 Distance restraints involve hydrogen bonds, and 44 dihedral angle restraints. | Felix |
NMR Ensemble Information | |
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Conformer Selection Criteria | Submitted conformers include average from molecular dynamics and 3 representative diverging structures. |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 4 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | The structure was determined using standard 2D homonuclear techniques. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | Felix | 98 | Biosym |
2 | structure solution | Amber | 4.1 | Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A. |
3 | refinement | Amber | 4.1 | Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A. |