2vql: 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:2vql.png|left|200px]]
-<!--
+==Crystal structure of PorB from Corynebacterium glutamicum (crystal form III)==
-The line below this paragraph, containing "STRUCTURE_2vql", creates the "Structure Box" on the page.
+<StructureSection load='2vql' size='340' side='right'caption='[[2vql]], [[Resolution|resolution]] 3.16&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'>[[2vql]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VQL 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]] 3.16&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2vql|  PDB=2vql  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vql OCA], [https://pdbe.org/2vql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vql RCSB], [https://www.ebi.ac.uk/pdbsum/2vql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vql ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8NRS3_CORGL Q8NRS3_CORGL]
+== 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/vq/2vql_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2vql ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The cell wall of Corynebacterium glutamicum contains a mycolic acid layer, which is a protective nonpolar barrier similar to the outer membrane of Gram-negative bacteria. The exchange of material across this barrier requires porins. Porin B (PorB) is one of them. Recombinant PorB has been produced in Escherichia coli, purified, crystallized and analyzed by X-ray diffraction, yielding 16 independent molecular structures in four different crystal forms at resolutions up to 1.8 A. All 16 molecules have the same globular core, which consists of 70 residues forming four alpha-helices tied together by a disulfide bridge. The 16 structures vary greatly with respect to the 29 residues in the N- and C-terminal extensions. Since corynebacteria belong to the group of mycolata that includes some prominent human pathogens, the observed structure may be of medical relevance. Due to the clearly established solid structure of the core, the native porin has to be oligomeric, and the reported structure is one of the subunits. An alpha-helical porin in a bacterial outer envelope is surprising because all presently known structures of such porins consist of beta-barrels. Since none of the four crystal packing arrangements was compatible with an oligomeric membrane channel, we constructed a model of such an oligomer that was consistent with all available data of native PorB. The proposed model is based on the required polar interior and nonpolar exterior of the porin, on a recurring crystal packing contact around a 2-fold axis, on the assumption of a simple C(n) symmetry (a symmetric arrangement around an n-fold axis), on the experimentally established electric conductivity and anion selectivity and on the generally observed shape of porin channels.
-===CRYSTAL STRUCTURE OF PORB FROM CORYNEBACTERIUM GLUTAMICUM (CRYSTAL FORM III)===
+A putative alpha-helical porin from Corynebacterium glutamicum.,Ziegler K, Benz R, Schulz GE J Mol Biol. 2008 Jun 6;379(3):482-91. Epub 2008 Apr 11. PMID:18462756<ref>PMID:18462756</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18462756}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vql" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18462756 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18462756}}
+__TOC__
+</StructureSection>
-==About this Structure==
-VQL is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VQL OCA].
-==Reference==
-<ref group="xtra">PMID:18462756</ref><references group="xtra"/>
 [[Category: Corynebacterium glutamicum]]
-[[Category: Benz, R.]]
+[[Category: Large Structures]]
-[[Category: Schulz, G E.]]
+[[Category: Benz R]]
-[[Category: Ziegler, K.]]
+[[Category: Schulz GE]]
-[[Category: Ion transport]]
+[[Category: Ziegler K]]
-[[Category: Membrane]]
-[[Category: Membrane protein]]
-[[Category: Porin]]
-[[Category: Transmembrane]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:22:49 2009''