The reconstruction of atomic co-ordinates from a protein stereo ribbon diagram when additional information for sufficient sidechain positions is available

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Abstract

Summary

We describe the application of a method for the reconstruction of three-dimensional atomic co-ordinates from a stereo ribbon diagram of a protein when additional information for some of the sidechain positions is available. The method has applications in cases where the 3D co-ordinates have not been made available by any means other than the original publication and are of interest as models for molecular replacement, homology modelling etc. The approach is, on the one hand, more general than other methods which are based on stereo figures which present specific atomic positions, but on the other hand relies on input from a specialist. Its exact implementation will depend on the figure of interest. We have applied the method to the case of the α-d-galactose-binding lectin jacalin with a resultant RMS deviation, compared to the crystal structure, of 1.5 Å for the 133 Cα positions of the α-chain and 2.6 Å for the less regular β-chain. The success of the method depends on the secondary structure of the protein under consideration and the orientation of the stereo diagram itself but can be expected to reproduce the mainchain co-ordinates more accurately than the sidechains. Some ways in which the method may be generalised to other cases are discussed.

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