This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2q3m

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:52, 29 August 2018

Ensemble refinement of the protein crystal structure of an Arabidopsis thaliana putative steroid sulphotransferase

Structural highlights

2q3m is a 1 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1q44
Gene:	At2g03760, F19B11.21 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SOT12_ARATH] Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the stereospecific sulfate conjugation of 24-epibrassinosteroids. Preferred substrates are 24-epicathasterone and 6-deoxo-24-epicathasterone. Low activity with 22-deoxy-24-epiteasterone. No activity with 24-epimers catasterone and brassinolide. Sulfonates salicylic acid. May be involved in detoxification. Enhances plant response to pathogen infection and contributes to long distance signaling in systemic acquired resistance (SAR).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Marsolais F, Boyd J, Paredes Y, Schinas AM, Garcia M, Elzein S, Varin L. Molecular and biochemical characterization of two brassinosteroid sulfotransferases from Arabidopsis, AtST4a (At2g14920) and AtST1 (At2g03760). Planta. 2007 Apr;225(5):1233-44. Epub 2006 Oct 13. PMID:17039368 doi:http://dx.doi.org/10.1007/s00425-006-0413-y
↑ Baek D, Pathange P, Chung JS, Jiang J, Gao L, Oikawa A, Hirai MY, Saito K, Pare PW, Shi H. A stress-inducible sulphotransferase sulphonates salicylic acid and confers pathogen resistance in Arabidopsis. Plant Cell Environ. 2010 Aug 1;33(8):1383-92. doi:, 10.1111/j.1365-3040.2010.02156.x. Epub 2010 Apr 1. PMID:20374532 doi:http://dx.doi.org/10.1111/j.1365-3040.2010.02156.x
↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q3m"

@@ Line 1: / Line 1: @@
 ==Ensemble refinement of the protein crystal structure of an Arabidopsis thaliana putative steroid sulphotransferase==
 <StructureSection load='2q3m' size='340' side='right' caption='[[2q3m]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1q44|1q44]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At2g03760, F19B11.21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3m OCA], [http://pdbe.org/2q3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q3m RCSB], [http://www.ebi.ac.uk/pdbsum/2q3m PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3m OCA], [http://pdbe.org/2q3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q3m RCSB], [http://www.ebi.ac.uk/pdbsum/2q3m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3m ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q3/2q3m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q3/2q3m_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

2q3m

From Proteopedia

Revision as of 08:52, 29 August 2018

Ensemble refinement of the protein crystal structure of an Arabidopsis thaliana putative steroid sulphotransferase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox