PMC:2728246 / 49616-51000
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/2728246","sourcedb":"PMC","sourceid":"2728246","source_url":"https://www.ncbi.nlm.nih.gov/pmc/2728246","text":"In recent years, a number of independent computational ensembles have been calculated to fulfill both structural restraints and dynamical information (Clore and Schwieters 2004, 2006; Markwick et al. 2007; Lindorff-Larsen et al. 2005; Richter et al. 2007; Lange et al. 2008; Friedland et al. 2009). From a number of available ubiquitin ensembles, we have back-calculated the average spherical harmonics and related MF parameters and compared them to the new data presented in this study. Thus, further insight into the conformations adopted by the side chains, especially in the ns-ms time scale can be obtained. Data for the ensembles of structures used here are presented in the Table 3.\nTable 3 Conformational heterogeneity for methyl groups from the average structure and dynamic ensembles of ubiquitin and correlation with RDC-derived average spherical harmonics\nPDB Number of conformers Positional rmsd of all methyl group carbons Av ± st dev order parameter Pearson correlation (\u003cY2,M\u003e) rmsd (\u003cY2,M\u003e) References\n1d3z 10 0.54 ± 0.23 Å 0.87 ± 0.19 0.8379 0.0758 Cornilescu et al. (1998)\n1xqq 128 1.76 ± 0.32 Å 0.59 ± 0.27 0.8497 0.0597 Lindorff-Larsen et al. (2005)\n2nr2 144 1.43 ± 0.24 Å 0.66 ± 0.21 0.8748 0.0588 Richter et al. (2007)\n2k39 116 2.28 ± 0.43 Å 0.45 ± 0.29 0.8568 0.0496 Lange et al. (2008)\n«brub» 50 1.77 ± 0.28 Å 0.59 ± 0.26 0.8092 0.0648 Friedland et al. 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