Abstract
This paper describes the structure of bovine pancreatic ribonuclease A, refined by a restrained parameter least squares procedure at 2.0 A resolution, and rebuilt using computer graphics. The final agreement factor (formula see text) is 0.159. The positions of the 951 main chain atoms have been determined with an estimated accuracy of 0.17 A. In addition, the model includes a phosphate group in the active site and 176 waters, many of them with partial occupancy. The bond lengths in the refined structure of RNase A differ from the ideal values by an overall root mean square deviation of 0.022 A; the corresponding value for angle distances is 0.06 A. The root mean square deviation of planar atoms from ideality is 0.017 A, and root mean square deviation of the peptide torsion angles from 180 degrees is 3.4 degrees. The model is in good agreement with the final difference Fourier maps. Two active site histidines, His 12 and His 119, form hydrogen bonds to the phosphate ion. His 119 is also hydrogen bonded to the carboxyl of ASp 121 and His 12 to the carbonyl of Thr 45. The structure of the RNase A is very similar to that of RNase S, particularly in the active site region. The root mean square discrepancy of all atoms from residues 1 to 16 and 24 to 123 is 1.06 A and the root mean square discrepancy for the active site region is 0.6 A.
Highlights
Baker, 1980; Phillips, 1980),we have decided to continue the refinement using the data extending to 2.0 A with the aim of the an 951 main chain atoms have been determined with estimated accuracyof 0.17A.In addition, the model providing a starting model more vestigation of both native RNase suitable and of for the subsequent ininhibitor comincludes a phosphate groupin the active site and 176 plexes by both x-ray and neutron diffraction techniques
The details of the procedures followed in this work are very similar those used for the refinement at 2.5 b, resolution (Wlodawer, 1980). order to keep the x-ray analysis compatible with the concurrent planar atoms from ideality is 0.017 and root mean neutron analysis, crystals from the same preparations were used for squaredeviation ofthepeptidetorsion angles from both investigations
180”is 3.4”.The model is in good agreement with the to decrease the incoherent scattering of the neutrons.Crystals of final difference Fourier maps
Summary
The computational procedure followed in2.0 A refinement did not differ appreciably from the one used previously (Wlodawer, 1980). Cohen (National Insti- considered the possibility that a map calculated after removal tutes of Health) for a VAX11/780 computer This version of of a protein fragment from phase calculation may still be the program included the restraints on nonbonded contact biased by the residual error introduced by the model used in distances, on chwal volumes of asymmetric carbon atoms, and refinement. To test this hypothesis, we removed the coordion thermal parameters of bonded atoms, as well as variable nates for residues 17-24 and ran seven cycles of refinement occupancy factors.The program was capable of the refinement for a model consistingof amino acids 1-16 and 25-124, as well of hydrogen positions and of utilizing neutron diffraction data, as all the solvent. Comparison of the selectedparameters for theinitial and final models of ribonucleasestructure
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
