1ndj: Difference between revisions

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-{{Seed}}
-[[Image:1ndj.png|left|200px]]
-<!--
+==Streptavidin Mutant Y43F with Biotin at 1.81A Resolution==
-The line below this paragraph, containing "STRUCTURE_1ndj", creates the "Structure Box" on the page.
+<StructureSection load='1ndj' size='340' side='right'caption='[[1ndj]], [[Resolution|resolution]] 1.81&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'>[[1ndj]] 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=1NDJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NDJ 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]] 1.81&#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_1ndj|  PDB=1ndj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ndj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndj OCA], [https://pdbe.org/1ndj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ndj RCSB], [https://www.ebi.ac.uk/pdbsum/1ndj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndj 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/nd/1ndj_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=1ndj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An elaborate hydrogen-bonding network contributes to the tight binding of biotin to streptavidin. The specific energetic contributions of hydrogen bonds to the biotin ureido oxygen have previously been investigated by mapping the equilibrium and activation thermodynamic signatures of N23A, N23E, S27A, Y43A and Y43F site-directed mutants [Klumb et al. (1998), Biochemistry, 37, 7657-7663]. The crystal structures of these variants in the unbound and biotin-bound states provide structural insight into the energetic alterations and are described here. High (1.5-2.2 A) to atomic resolution (1.14 A) structures were obtained and structural models were refined to R values ranging from 0.12 to 0.20. The overall folding of streptavidin as described previously has not changed in any of the mutant structures. Major deviations such as side-chain shifts of residues in the binding site are observed only for the N23A and Y43A mutations. In none of the mutants is a systematic shift of biotin observed when one of the hydrogen-bonding partners to the ureido oxygen of biotin is removed. Recent thermodynamic studies report increases of DeltaDeltaG(o) of 5.0-14.6 kJ mol(-1) for these mutants with respect to the wild-type protein. The decreasing stabilities of the complexes of the mutants are discussed in terms of their structures.
-===Streptavidin Mutant Y43F with Biotin at 1.81A Resolution===
+Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin.,Le Trong I, Freitag S, Klumb LA, Chu V, Stayton PS, Stenkamp RE Acta Crystallogr D Biol Crystallogr. 2003 Sep;59(Pt 9):1567-73. Epub 2003, Aug 19. PMID:12925786<ref>PMID:12925786</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ndj" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12925786}}, adds the Publication Abstract to the page
+*[[Avidin 3D structures|Avidin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12925786 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12925786}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-NDJ is a 4 chains structure of sequences 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=1NDJ OCA].
-==Reference==
-<ref group="xtra">PMID:12925786</ref><references group="xtra"/>
 [[Category: Streptomyces avidinii]]
-[[Category: Chu, V.]]
+[[Category: Chu V]]
-[[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: Tetramer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:50:11 2009''