1swr: Difference between revisions

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-[[Image:1swr.png|left|200px]]
-<!--
+==CORE-STREPTAVIDIN MUTANT W120A IN COMPLEX WITH BIOTIN AT PH 7.5==
-The line below this paragraph, containing "STRUCTURE_1swr", creates the "Structure Box" on the page.
+<StructureSection load='1swr' size='340' side='right'caption='[[1swr]], [[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'>[[1swr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SWR 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTN:BIOTIN'>BTN</scene></td></tr>
-{{STRUCTURE_1swr|  PDB=1swr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1swr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1swr OCA], [https://pdbe.org/1swr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1swr RCSB], [https://www.ebi.ac.uk/pdbsum/1swr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1swr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).
+== 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/sw/1swr_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=1swr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Previous thermodynamic and computational studies have pointed to the important energetic role of aromatic contacts in generating the exceptional binding free energy of streptavidin-biotin association. We report here the crystallographic characterization of single site tryptophan mutants in investigating structural consequences of alterations in these aromatic contacts. Four tryptophan residues, Trp79, Trp92, Trp108 and Trp120, play an important role in the hydrophobic binding contributions, which along with a hydrogen bonding network and a flexible binding loop give rise to tight ligand binding (Ka approximately 10(13) M-1). The crystal structures of ligand-free and biotin-bound mutants, W79F, W108F, W120F and W120A, in the resolution range from 1.9 to 2.3 A were determined. Nine data sets for these four different mutants were collected, and structural models were refined to R-values ranging from 0.15 to 0.20. The major question addressed here is how these mutations influence the streptavidin binding site and in particular how they affect the binding mode of biotin in the complex. The overall folding of streptavidin was not significantly altered in any of the tryptophan mutants. With one exception, only minor deviations in the unbound structures were observed. In one crystal form of unbound W79F, there is a coupled shift in the side-chains of Phe29 and Tyr43 toward the mutation site, although in a different crystal form these shifts are not observed. In the bound structures, the orientation of biotin in the binding pocket was not significantly altered in the mutant complex. Compared with the wild-type streptavidin-biotin complex, there were no additional crystallographic water molecules observed for any of the mutants in the binding pocket. These structural studies thus suggest that the thermodynamic alterations can be attributed to the local alterations in binding residue composition, rather than a rearrangement of binding site architectures.
-===CORE-STREPTAVIDIN MUTANT W120A IN COMPLEX WITH BIOTIN AT PH 7.5===
+Structural studies of binding site tryptophan mutants in the high-affinity streptavidin-biotin complex.,Freitag S, Le Trong I, Chilkoti A, Klumb LA, Stayton PS, Stenkamp RE J Mol Biol. 1998 May 29;279(1):211-21. PMID:9636711<ref>PMID:9636711</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_9636711}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1swr" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 9636711 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_9636711}}
-==About this Structure==
-[[1swr]] is a 4 chain structure of [[Avidin]] with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SWR OCA].
 ==See Also==
-*[[Avidin]]
+*[[Avidin 3D structures|Avidin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:9636711</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces avidinii]]
-[[Category: Chilkoti, A.]]
+[[Category: Chilkoti A]]
-[[Category: Freitag, S.]]
+[[Category: Freitag S]]
-[[Category: Klumb, L A.]]
+[[Category: Klumb LA]]
-[[Category: Stayton, P S.]]
+[[Category: Le Trong I]]
-[[Category: Stenkamp, R E.]]
+[[Category: Stayton PS]]
-[[Category: Trong, I Le.]]
+[[Category: Stenkamp RE]]
-[[Category: Biotin-binding protein]]