2exs: Difference between revisions

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-{{Seed}}
-[[Image:2exs.png|left|200px]]
-<!--
+==TRAP3 (engineered TRAP)==
-The line below this paragraph, containing "STRUCTURE_2exs", creates the "Structure Box" on the page.
+<StructureSection load='2exs' size='340' side='right'caption='[[2exs]], [[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'>[[2exs]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXS 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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
-{{STRUCTURE_2exs|  PDB=2exs  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2exs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exs OCA], [https://pdbe.org/2exs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exs RCSB], [https://www.ebi.ac.uk/pdbsum/2exs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exs ProSAT]</span></td></tr>
+</table>
+== 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/ex/2exs_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=2exs ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The protein TRAP (trp RNA binding attenuation protein) forms a highly thermostable ring-shaped 11-mer. By linking in tandem two, three, or four DNA sequences encoding TRAP monomers, we have engineered new rings that consist of 12 TRAP subunits and bind 12 ligand molecules. The hydrogen bonding pattern and buried surface area within and between subunits are essentially identical between the 11-mer and 12-mer crystal structures. Why do the artificial proteins choose to make single 12-mer rings? The 12-mer rings are highly sterically strained by their peptide linkers and far from thermostable. That proteins choose to adopt a strained conformation of few subunits rather than an unstrained one with 11 subunits demonstrates the importance of entropic factors in controlling protein-protein interactions in general.
-===TRAP3 (engineered TRAP)===
+Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP.,Heddle JG, Yokoyama T, Yamashita I, Park SY, Tame JR Structure. 2006 May;14(5):925-33. PMID:16698553<ref>PMID:16698553</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2exs" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16698553}}, adds the Publication Abstract to the page
+*[[Tryptophan RNA-binding attenuation protein|Tryptophan RNA-binding attenuation protein]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16698553 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16698553}}
+__TOC__
+</StructureSection>
-==About this Structure==
-EXS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXS OCA].
-==Reference==
-Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP., Heddle JG, Yokoyama T, Yamashita I, Park SY, Tame JR, Structure. 2006 May;14(5):925-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16698553 16698553]
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Heddle, J G.]]
+[[Category: Heddle JG]]
-[[Category: Park, S Y.]]
+[[Category: Park SY]]
-[[Category: Tame, J R.H.]]
+[[Category: Tame JRH]]
-[[Category: Yamashita, I.]]
+[[Category: Yamashita I]]
-[[Category: Yokoyama, T.]]
+[[Category: Yokoyama T]]
-[[Category: 12-mer]]
-[[Category: Artificial]]
-[[Category: Engineered]]
-[[Category: Ring protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:25:34 2008''