1vjl: Difference between revisions

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-{{Seed}}
-[[Image:1vjl.png|left|200px]]
-<!--
+==Crystal structure of a duf151 family protein (tm0160) from thermotoga maritima at 1.90 A resolution==
-The line below this paragraph, containing "STRUCTURE_1vjl", creates the "Structure Box" on the page.
+<StructureSection load='1vjl' size='340' side='right'caption='[[1vjl]], [[Resolution|resolution]] 1.90&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'>[[1vjl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1o5y 1o5y]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VJL FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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=1vjl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vjl OCA], [https://pdbe.org/1vjl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vjl RCSB], [https://www.ebi.ac.uk/pdbsum/1vjl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vjl ProSAT], [https://www.topsan.org/Proteins/JCSG/1vjl TOPSAN]</span></td></tr>
-{{STRUCTURE_1vjl|  PDB=1vjl  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9WY07_THEMA Q9WY07_THEMA]
+== 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/vj/1vjl_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=1vjl ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of two Thermotoga maritima proteins, a conserved hypothetical protein (TM0160) and a transcriptional regulator (TM1171), have now been determined at 1.9 A and 2.3 A resolution, respectively, as part of a large-scale structural genomics project. Our first efforts to crystallize full-length versions of these targets were unsuccessful. However, analysis of the recombinant purified proteins using the technique of enhanced amide hydrogen/deuterium exchange mass spectroscopy (DXMS) revealed substantial regions of rapid amide deuterium hydrogen exchange, consistent with flexible regions of the structures. Based on these exchange data, truncations were designed to selectively remove the disordered C-terminal regions, and the resulting daughter proteins showed greatly enhanced crystallizability. Comparative DXMS analysis of full-length protein versus truncated forms demonstrated complete and exact preservation of the exchange rate profiles in the retained sequence, indicative of conservation of the native folded structure. This study presents the first structures produced with the aid of the DXMS method for salvaging intractable crystallization targets. The structure of TM0160 represents a new fold and highlights the use of this approach where any prior structural knowledge is absent. The structure of TM1171 represents an example where the lack of a substrate/cofactor may impair crystallization. The details of both structures are presented and discussed.
-===CRYSTAL STRUCTURE OF PREDICTED PROTEIN RELATED TO WOUND INDUCIVE PROTEINS IN PLANTS (TM0160) FROM THERMOTOGA MARITIMA AT 1.90 A RESOLUTION===
+On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171.,Spraggon G, Pantazatos D, Klock HE, Wilson IA, Woods VL Jr, Lesley SA Protein Sci. 2004 Dec;13(12):3187-99. PMID:15557262<ref>PMID:15557262</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_15557262}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1vjl" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15557262 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15557262}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VJL is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1o5y 1o5y]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJL OCA].
-==Reference==
-<ref group="xtra">PMID:15557262</ref><references group="xtra"/>
 [[Category: Thermotoga maritima]]
-[[Category: Genomics, Joint Center for Structural.]]
-[[Category: JCSG, Joint Center for Structural Genomics.]]
-[[Category: Jcsg]]
-[[Category: Joint center for structural genomic]]
-[[Category: Predicted protein related to wound inducive proteins in plant]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
 [[Category: Structural genomic]]
-[[Category: Tm0160]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 03:47:01 2009''