2AAI

Crystallographic refinement of ricin to 2.5 Angstroms

Summary for 2AAI

• Entry DOI: 10.2210/pdb2aai/pdb
• Related PRD ID: PRD_900004
• Descriptor: RICIN (A CHAIN), RICIN (B CHAIN), beta-D-galactopyranose-(1-4)-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: glycosidase, hydrolase
• Biological source: Ricinus communis (castor bean)
• Total number of polymer chains: 2
• Total formula weight: 61432.58

Authors

Rutenber, E.,Katzin, B.J.,Montfort, W.,Villafranca, J.E.,Ernst, S.R.,Collins, E.J.,Mlsna, D.,Monzingo, A.F.,Ready, M.P.,Robertus, J.D. (deposition date: 1993-09-07, release date: 1994-01-31, Last modification date: 2024-11-13)

Primary citation

Rutenber, E.,Katzin, B.J.,Ernst, S.,Collins, E.J.,Mlsna, D.,Ready, M.P.,Robertus, J.D.
Crystallographic refinement of ricin to 2.5 A.
Proteins, 10:240-250, 1991

PubMed Abstract: 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.

PubMed: 1881880
DOI: 10.1002/prot.340100308

Experimental method

X-RAY DIFFRACTION (2.5 Å)