2v93: Difference between revisions

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-{{Seed}}
-[[Image:2v93.png|left|200px]]
-<!--
+==EQUILLIBRIUM MIXTURE OF OPEN AND PARTIALLY-CLOSED SPECIES IN THE APO STATE OF MALTODEXTRIN-BINDING PROTEIN BY PARAMAGNETIC RELAXATION ENHANCEMENT NMR==
-The line below this paragraph, containing "STRUCTURE_2v93", creates the "Structure Box" on the page.
+<StructureSection load='2v93' size='340' side='right'caption='[[2v93]]' 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'>[[2v93]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V93 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">Solution NMR, 50 models</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MXT:1-(1-HYDROXY-2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)PYRROLIDINE-2,5-DIONE'>MXT</scene></td></tr>
-{{STRUCTURE_2v93|  PDB=2v93  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v93 OCA], [https://pdbe.org/2v93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v93 RCSB], [https://www.ebi.ac.uk/pdbsum/2v93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v93 ProSAT]</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/v9/2v93_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=2v93 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation. Crystal structures have provided a static picture of the apo (usually open) and holo usually closed) states. The general question arises as to whether the apo state exists as a single species in which the closed state is energetically inaccessible and interdomain rearrangement is induced by ligand or substrate binding, or whether the predominantly open form already coexists in rapid equilibrium with a minor closed species. The maltose-binding protein (MBP), a member of the bacterial periplasmic binding protein family, provides a model system for investigating this problem because it has been the subject of extensive studies by crystallography, NMR and other biophysical techniques. Here we show that although paramagnetic relaxation enhancement (PRE) data for the sugar-bound form are consistent with the crystal structure of holo MBP, the PRE data for the apo state are indicative of a rapidly exchanging mixture (ns to mus regime) of a predominantly ( approximately 95%) open form (represented by the apo crystal structure) and a minor (approximately 5%) partially closed species. Using ensemble simulated annealing refinement against the PRE data we are able to determine a &lt;r(-6)&gt; ensemble average structure of the minor apo species and show that it is distinct from the sugar-bound state.
-===EQUILLIBRIUM MIXTURE OF OPEN AND PARTIALLY-CLOSED SPECIES IN THE APO STATE OF MALTODEXTRIN-BINDING PROTEIN BY PARAMAGNETIC RELAXATION ENHANCEMENT NMR===
+Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR.,Tang C, Schwieters CD, Clore GM Nature. 2007 Oct 25;449(7165):1078-82. PMID:17960247<ref>PMID:17960247</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2v93" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17960247}}, adds the Publication Abstract to the page
+*[[Maltose-binding protein 3D structures|Maltose-binding protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17960247 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17960247}}
+__TOC__
+</StructureSection>
-==About this Structure==
-V93 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V93 OCA].
-==Reference==
-Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR., Tang C, Schwieters CD, Clore GM, Nature. 2007 Oct 25;449(7165):1078-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17960247 17960247]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Clore, G M.]]
+[[Category: Clore GM]]
-[[Category: Tang, C.]]
+[[Category: Tang C]]
-[[Category: Domain motion]]
-[[Category: Mbp]]
-[[Category: Minor species in solution]]
-[[Category: Periplasm]]
-[[Category: Pre]]
-[[Category: Rapid conformational exchange]]
-[[Category: Sugar transport]]
-[[Category: Transport]]
-[[Category: Transport protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 23:34:17 2008''