Bioc585 2008 Exercise 6 – Structure Factors from the PDB Homework due Tuesday, May 6 Homework 6 – 10 points 1. For structure 1XA5, include a snapshot of the geometry vs. refinement cycle graph from Refmac. Should look something like the graph on the left. 2. For structure 1XA5, describe the linking domain (“central helix”) in the model and the electron density for this region. Include a snapshot to illustrate your conclusions regarding geometry and structure quality. The central helix becomes disordered and kinked, such that the calcium binding domains move closer together. Two residues (75-76) are so disordered that they were not included in the model (above, right).3. For structure 1XA5, calculate an “omit” map for either the linking domain or the inhibitor, and include a snapshot of the result. Is the omitted portion well represented? The linker is essentially already omitted, since residues 75-76 are missing in the model. The difference map for this region is essentially blank (figure above), supporting the author’s decision to omit these residues. 4. On comparing 1XA5 and 1CDL, do the bound helix and the bound inhibitor occupy similar places in calmodulin? Do they induce similar calmodulin conformations? Include a snapshot. The helix (cyan) and the inhibitor are coincident (left panel). The conformations of the two complexes are similar but exactly the same (middle panel). 5. How many calmodulin molecules are in the asymmetric unit of 1CDL? How well do the A and B molecules compare? There are four calmodulin molecules in the asymmetric unit and four in the PDB file. Although there are no constraints on the asymmetric unit requiring that the four versions adopt the same conformation, all four appear at first glance to be the same. Comparison of the A and B molecules using SSM confirms that the two are nearly identical (right panel above). The RMS deviation among the core atoms used for superpositioning is 0.64
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