2aai: Difference between revisions
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==Overview== | ==Overview== | ||
The plant cytotoxin ricin consists of two disulfide-linked chains, each of | 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. | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: rRNA N-glycosylase]] | [[Category: rRNA N-glycosylase]] | ||
[[Category: Collins, E | [[Category: Collins, E J.]] | ||
[[Category: Ernst, S | [[Category: Ernst, S R.]] | ||
[[Category: Katzin, B | [[Category: Katzin, B J.]] | ||
[[Category: Mlsna, D.]] | [[Category: Mlsna, D.]] | ||
[[Category: Montfort, W.]] | [[Category: Montfort, W.]] | ||
[[Category: Monzingo, A | [[Category: Monzingo, A F.]] | ||
[[Category: Ready, M | [[Category: Ready, M P.]] | ||
[[Category: Robertus, J | [[Category: Robertus, J D.]] | ||
[[Category: Rutenber, E.]] | [[Category: Rutenber, E.]] | ||
[[Category: Villafranca, J | [[Category: Villafranca, J E.]] | ||
[[Category: glycosidase]] | [[Category: glycosidase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:25:30 2008'' | ||
Revision as of 17:25, 21 February 2008
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CRYSTALLOGRAPHIC REFINEMENT OF RICIN TO 2.5 ANGSTROMS
OverviewOverview
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.
About this StructureAbout this Structure
2AAI is a Single protein structure of sequence from [1]. The following page contains interesting information on the relation of 2AAI with [Cholera Toxin]. Active as rRNA N-glycosylase, with EC number 3.2.2.22 Full crystallographic information is available from OCA.
ReferenceReference
Crystallographic refinement of ricin to 2.5 A., Rutenber E, Katzin BJ, Ernst S, Collins EJ, Mlsna D, Ready MP, Robertus JD, Proteins. 1991;10(3):240-50. PMID:1881880
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