The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 A MIR electron density map has been refined against 2.5 A data using rounds of hand rebuilding coupled with either a restrained least squares algorithm or molecular dynamics (XPLOR) ...
The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 A MIR electron density map has been refined against 2.5 A data using rounds of hand rebuilding coupled with either a restrained least squares algorithm or molecular dynamics (XPLOR). The last model (9) has an R factor of 21.6% and RMS deviations from standard bond lengths and angles of 0.021 A and 4.67 degrees, respectively. Refinement required several peptide segments in the original model to be adjusted translationally along the electron density. A wide range of lesser changes were also made. The RMS deviation of backbone atoms between the original and model 9 was 1.89 A. Molecular dynamics proved to be a very powerful refinement tool. However, tests showed that it could not replace human intervention in making adjustments such as local translations of the peptide chain. The R factor is not a completely satisfactory indicator of refinement progress; difference Fouriers, when observed carefully, may be a better monitor.
Related Citations:
Structure of Ricin A-Chain at 2.5 Angstroms Katzin, B.J., Collins, E.J., Robertus, J.D. (1991) Proteins 10: 251
Structure of Ricin B-Chain at 2.5 Angstroms Rutenber, E., Robertus, J.D. (1991) Proteins 10: 260
The Three-Dimensional Structure of Ricin at 2.8 Angstroms Montfort, W., Villafranca, J.E., Monzingo, A.F., Ernst, S.R., Katzin, B., Rutenber, E., Xuong, N.H., Hamlin, R., Robertus, J.D. (1987) J Biol Chem 262: 5398
Organizational Affiliation:
Clayton Foundation Biochemical Institute, Department of Chemistry and Biochemistry, University of Texas, Austin 78712.
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