2pfs: Difference between revisions

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-[[Image:2pfs.png|left|200px]]
-<!--
+==Crystal structure of universal stress protein from Nitrosomonas europaea==
-The line below this paragraph, containing "STRUCTURE_2pfs", creates the "Structure Box" on the page.
+<StructureSection load='2pfs' size='340' side='right'caption='[[2pfs]], [[Resolution|resolution]] 2.25&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'>[[2pfs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Niteu Niteu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PFS 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></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2pfs|  PDB=2pfs  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NE1028 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=228410 NITEU])</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=2pfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pfs OCA], [https://pdbe.org/2pfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pfs RCSB], [https://www.ebi.ac.uk/pdbsum/2pfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pfs ProSAT], [https://www.topsan.org/Proteins/MCSG/2pfs TOPSAN]</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/pf/2pfs_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=2pfs ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We present the crystal structures of two universal stress proteins (USP) from Archaeoglobus fulgidus and Nitrosomonas europaea in both apo- and ligand-bound forms. This work is the first complete synthesis of the structural properties of 26 USP available in the Protein Data Bank, over 75% of which were determined by structure genomics centers with no additional information provided. The results of bioinformatic analyses of all available USP structures and their sequence homologs revealed that these two new USP structures share overall structural similarity with structures of USPs previously determined. Clustering and cladogram analyses, however, show how they diverge from other members of the USP superfamily and show greater similarity to USPs from organisms inhabiting extreme environments. We compared them with other archaeal and bacterial USPs and discuss their similarities and differences in context of structure, sequential motifs, and potential function. We also attempted to group all analyzed USPs into families, so that assignment of the potential function to those with no experimental data available would be possible by extrapolation.
-===Crystal structure of universal stress protein from Nitrosomonas europaea===
+Structural and functional insight into the universal stress protein family.,Tkaczuk KL, A Shumilin I, Chruszcz M, Evdokimova E, Savchenko A, Minor W Evol Appl. 2013 Apr;6(3):434-49. doi: 10.1111/eva.12057. Epub 2013 Mar 13. PMID:23745136<ref>PMID:23745136</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[2pfs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Nitrosomonas_europaea_atcc_19718 Nitrosomonas europaea atcc 19718]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PFS OCA].
+<div class="pdbe-citations 2pfs" style="background-color:#fffaf0;"></div>
-[[Category: Nitrosomonas europaea atcc 19718]]
+== References ==
-[[Category: Chruszcz, M.]]
+<references/>
-[[Category: Cymborowski, M.]]
+__TOC__
-[[Category: Edwards, A.]]
+</StructureSection>
-[[Category: Evdokimova, E.]]
+[[Category: Large Structures]]
-[[Category: Joachimiak, A.]]
+[[Category: Niteu]]
-[[Category: Kagan, O.]]
+[[Category: Chruszcz, M]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Cymborowski, M]]
-[[Category: Minor, W.]]
+[[Category: Edwards, A]]
-[[Category: Savchenko, A.]]
+[[Category: Evdokimova, E]]
+[[Category: Joachimiak, A]]
+[[Category: Kagan, O]]
+[[Category: Structural genomic]]
+[[Category: Minor, W]]
+[[Category: Savchenko, A]]
 [[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
+[[Category: PSI, Protein structure initiative]]
-[[Category: Protein structure initiative]]
-[[Category: Psi-2]]
 [[Category: Stress protein]]
-[[Category: Structural genomic]]
 [[Category: Unknown function]]