1gic: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1gic.png|left|200px]]
-<!--
+==CONCANAVALIN A COMPLEXED WITH METHYL ALPHA-D-GLUCOPYRANOSIDE==
-The line below this paragraph, containing "STRUCTURE_1gic", creates the "Structure Box" on the page.
+<StructureSection load='1gic' size='340' side='right'caption='[[1gic]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</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>
-{{STRUCTURE_1gic|  PDB=1gic  |  SCENE=  }}
+<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.
-===CONCANAVALIN A COMPLEXED WITH METHYL ALPHA-D-GLUCOPYRANOSIDE===
+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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1gic" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15299735}}, adds the Publication Abstract to the page
+*[[Concanavalin 3D structures|Concanavalin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15299735 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15299735}}
+__TOC__
+</StructureSection>
-==About this Structure==
-GIC is a 2 chains structure of sequences from [http://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].
-==Reference==
-<ref group="xtra">PMID:15299735</ref><references group="xtra"/>
 [[Category: Canavalia ensiformis]]
-[[Category: Bradbrook, G M.]]
+[[Category: Large Structures]]
-[[Category: Gilboa, A J.Kalb.]]
+[[Category: Bradbrook GM]]
-[[Category: Gleichmann, T.]]
+[[Category: Gleichmann T]]
-[[Category: Habash, J.]]
+[[Category: Habash J]]
-[[Category: Harrop, S J.]]
+[[Category: Harrop SJ]]
-[[Category: Helliwell, J R.]]
+[[Category: Helliwell JR]]
-[[Category: Tong, L.]]
+[[Category: Tong L]]
-[[Category: Wan, T C.M.]]
+[[Category: Wan TCM]]
-[[Category: Yariv, J.]]
+[[Category: Yariv J]]
-[[Category: Complex]]
-[[Category: Lectin]]
-[[Category: Saccharide]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:45:06 2009''