2av9: Difference between revisions

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-[[Image:2av9.gif|left|200px]]
-<!--
+==Crystal Structure of the PA5185 protein from Pseudomonas Aeruginosa Strain PAO1.==
-The line below this paragraph, containing "STRUCTURE_2av9", creates the "Structure Box" on the page.
+<StructureSection load='2av9' size='340' side='right'caption='[[2av9]], [[Resolution|resolution]] 2.40&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'>[[2av9]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AV9 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]] 2.4&#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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2av9|  PDB=2av9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2av9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2av9 OCA], [https://pdbe.org/2av9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2av9 RCSB], [https://www.ebi.ac.uk/pdbsum/2av9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2av9 ProSAT], [https://www.topsan.org/Proteins/MCSG/2av9 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9HU04_PSEAE Q9HU04_PSEAE]
+== 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/av/2av9_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=2av9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of PA5185, a putative thioesterase from Pseudomonas aeruginosa strain PAO1, was solved using multi-wavelength anomalous diffraction to 2.4 A. Analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. The crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative PA5185 substrate (CoA or its derivative). Using new crystallization conditions containing this function-biased set of additives, several new crystal forms were produced and structures of three of them (in three different space groups) were determined. One of the new crystal forms had an improved resolution limit of 1.9 A, and another displayed an alternative conformation of the highly-conserved loop containing Asn26, which could play a physiological role. Surprisingly, none of the additives were ordered in the crystal structures. Application of function-biased additives could be used as a standard optimization protocol for producing improved diffraction, or new crystal forms, which may lead to better understanding of the biological functions of proteins.
-'''Crystal Structure of the PA5185 protein from Pseudomonas Aeruginosa Strain PAO1.'''
+Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1.,Chruszcz M, Zimmerman MD, Wang S, Koclega KD, Zheng H, Evdokimova E, Kudritska M, Cymborowski M, Savchenko A, Edwards A, Minor W Cryst Growth Des. 2008 Nov 5;8(11):4054-4061. PMID:19898606<ref>PMID:19898606</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2av9" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-AV9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AV9 OCA].
+*[[Thioesterase 3D structures|Thioesterase 3D structures]]
-[[Category: Pseudomonas aeruginosa]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Chruszcz, M.]]
+__TOC__
-[[Category: Cymborowski, M.]]
+</StructureSection>
-[[Category: Edwards, A.]]
+[[Category: Large Structures]]
-[[Category: Evdokimova, E.]]
+[[Category: Pseudomonas aeruginosa PAO1]]
-[[Category: Kudritska, M.]]
+[[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: Wang, S.]]
+[[Category: Joachimiak A]]
-[[Category: Mcsg]]
+[[Category: Kudritska M]]
-[[Category: Midwest center for structural genomic]]
+[[Category: Minor W]]
-[[Category: Protein structure initiative]]
+[[Category: Savchenko A]]
-[[Category: Psi]]
+[[Category: Wang S]]
-[[Category: Structural genomic]]
-[[Category: Thioesterase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 19:31:03 2008''