1gic: Difference between revisions
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==CONCANAVALIN A COMPLEXED WITH METHYL ALPHA-D-GLUCOPYRANOSIDE== | |||
<StructureSection load='1gic' size='340' side='right'caption='[[1gic]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1gic]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GIC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GIC FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GYP:METHYL-ALPHA-D-GLUCOPYRANOSIDE'>GYP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gic OCA], [https://pdbe.org/1gic PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gic RCSB], [https://www.ebi.ac.uk/pdbsum/1gic PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gic ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CONA_CANEN CONA_CANEN] D-mannose specific lectin. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gi/1gic_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gic ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The solution of the cubic crystal form (a = 167.8 A) of concanavalin A complexed with the monosaccharide methyl alpha-D-glucopyranoside is described. The space group has been determined as I2(1)3 rather than I23. The use of cadmium to replace cobalt at the transition metal-ion binding site and to replace calcium at its binding site proved to be crucial to the successful solution of the crystal structure. The relatively small isomorphous signals of 21 e(-) for the replacement of cobalt and 28 e(-) for the replacement of calcium, yielded interpretable difference Patterson maps. The electron-density map calculated in space group I2(1)3 at 5.4 A resolution, based on phases derived from single- and double-substituted cadmium differences, revealed a classical concanavalin A tetramer of 222 point symmetry, as seen in all the known crystal structures of concanavalin A. Rigid-body refinement at 3.6 A using the refined coordinates of saccharide-free concanavalin A converged to an R factor of 27.4%. A molecular-replacement analysis, consistent with this crystal structure, and initial experiences in the incorrect space group I23 are described as these also prove to be instructive. | |||
Structure solution of a cubic crystal of concanavalin A complexed with methyl alpha-D-glucopyranoside.,Harrop SJ, Helliwell JR, Wan TC, Kalb AJ, Tong L, Yariv J Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):143-55. PMID:15299735<ref>PMID:15299735</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1gic" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Concanavalin | *[[Concanavalin 3D structures|Concanavalin 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Canavalia ensiformis]] | [[Category: Canavalia ensiformis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Bradbrook GM]] | ||
[[Category: Gleichmann | [[Category: Gleichmann T]] | ||
[[Category: Habash | [[Category: Habash J]] | ||
[[Category: Harrop | [[Category: Harrop SJ]] | ||
[[Category: Helliwell | [[Category: Helliwell JR]] | ||
[[Category: Tong | [[Category: Tong L]] | ||
[[Category: Wan | [[Category: Wan TCM]] | ||
[[Category: Yariv | [[Category: Yariv J]] | ||
Latest revision as of 09:11, 9 August 2023
CONCANAVALIN A COMPLEXED WITH METHYL ALPHA-D-GLUCOPYRANOSIDECONCANAVALIN A COMPLEXED WITH METHYL ALPHA-D-GLUCOPYRANOSIDE
Structural highlights
FunctionCONA_CANEN D-mannose specific lectin. 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 PubMedThe solution of the cubic crystal form (a = 167.8 A) of concanavalin A complexed with the monosaccharide methyl alpha-D-glucopyranoside is described. The space group has been determined as I2(1)3 rather than I23. The use of cadmium to replace cobalt at the transition metal-ion binding site and to replace calcium at its binding site proved to be crucial to the successful solution of the crystal structure. The relatively small isomorphous signals of 21 e(-) for the replacement of cobalt and 28 e(-) for the replacement of calcium, yielded interpretable difference Patterson maps. The electron-density map calculated in space group I2(1)3 at 5.4 A resolution, based on phases derived from single- and double-substituted cadmium differences, revealed a classical concanavalin A tetramer of 222 point symmetry, as seen in all the known crystal structures of concanavalin A. Rigid-body refinement at 3.6 A using the refined coordinates of saccharide-free concanavalin A converged to an R factor of 27.4%. A molecular-replacement analysis, consistent with this crystal structure, and initial experiences in the incorrect space group I23 are described as these also prove to be instructive. Structure solution of a cubic crystal of concanavalin A complexed with methyl alpha-D-glucopyranoside.,Harrop SJ, Helliwell JR, Wan TC, Kalb AJ, Tong L, Yariv J Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):143-55. PMID:15299735[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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