Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum
Abstract
:1. Introduction
2. Results and Discussion
3. Experimental Section
3.1. Preparation of Protein Samples
3.2. NMR Spectroscopy and Data Collection
3.3. NMR Structure Calculation
4. Conclusions
Acknowledgments
References
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Conformationally-Restricting Constraints b | |
Distance Constraints | |
Intra-residue (I = j) | 306 |
Sequential (|i–j| = 1) | 357 |
Medium-range (1 < |i–j| < 5) | 193 |
Long-range (|i–j| ≥ 5) | 419 |
Total | 1275 |
Distance constraints per residue | 15.5 |
Hydrogen bond constraints | |
Long-range (|i–j| ≥ 5)/total | 20/56 |
Dihedral angle constraints | 92 |
Total number of restricting constraints | 1423 |
Number of constraints per residue | 5.4 |
Residue Constraint Violations b | |
Average Number of Distance Violations Per Structure | |
0.1–0.2 Å | 4.85 |
0.2–0.5 Å | 1.15 |
>0.5 Å | 0 |
Average RMS distance violation/constraint (Å) | 0.01 |
Maximum distance violation (Å) | 0.29 |
Average Number of Dihedral Angle Violations Per Structure | |
1–10° | 0.7 |
>10° | 0 |
Average RMS dihedral angle violation/constraint (degree) | 0.15 |
Maximum dihedral angle violation (degree) | 2.60 |
RMSD from Average Coordinates (Å) c | |
Backbone/Heavy atoms | 0.5/0.9 |
Ramachandran Plot Statistics c | |
Most favored regions (%) | 96.3 |
Additional allowed regions (%) | 3.6 |
Generously allowed (%) | 0.1 |
Disallowed regions (%) | 0 |
Global Quality Scores (raw/Z-score) b | |
Verify3D | 0.24/−3.53 |
Prosall | 0.30/−1.45 |
Procheck(phi-psi) c | 0.21/1.14 |
Procheck(all) c | 0.23/1.36 |
Molprobity clash | 16.49/−1.30 |
RPF Scores d | |
Recall | 0.98 |
Precision | 0.91 |
F-measure | 0.94 |
DP-score | 0.80 |
© 2012 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
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Yang, Y.; Ramelot, T.A.; Cort, J.R.; Garcia, M.; Yee, A.; Arrowsmith, C.H.; Kennedy, M.A. Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum. Int. J. Mol. Sci. 2012, 13, 7354-7364. https://doi.org/10.3390/ijms13067354
Yang Y, Ramelot TA, Cort JR, Garcia M, Yee A, Arrowsmith CH, Kennedy MA. Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum. International Journal of Molecular Sciences. 2012; 13(6):7354-7364. https://doi.org/10.3390/ijms13067354
Chicago/Turabian StyleYang, Yunhuang, Theresa A. Ramelot, John R. Cort, Maite Garcia, Adelinda Yee, Cheryl H. Arrowsmith, and Michael A. Kennedy. 2012. "Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum" International Journal of Molecular Sciences 13, no. 6: 7354-7364. https://doi.org/10.3390/ijms13067354
APA StyleYang, Y., Ramelot, T. A., Cort, J. R., Garcia, M., Yee, A., Arrowsmith, C. H., & Kennedy, M. A. (2012). Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum. International Journal of Molecular Sciences, 13(6), 7354-7364. https://doi.org/10.3390/ijms13067354