1do7: Difference between revisions

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-[[Image:1do7.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1do7", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1do7|  PDB=1do7  |  SCENE=  }}
-'''CARBONMONOXY-MYOGLOBIN (MUTANT L29W) REBINDING STRUCTURE AFTER PHOTOLYSIS AT T< 180K'''
+==CARBONMONOXY-MYOGLOBIN (MUTANT L29W) REBINDING STRUCTURE AFTER PHOTOLYSIS AT T< 180K==
+<StructureSection load='1do7' size='340' side='right'caption='[[1do7]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1do7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DO7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DO7 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PRD_900006:trehalose'>PRD_900006</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1do7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1do7 OCA], [https://pdbe.org/1do7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1do7 RCSB], [https://www.ebi.ac.uk/pdbsum/1do7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1do7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
+== 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/do/1do7_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=1do7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Myoglobin, a small globular haem protein that binds gaseous ligands such as O2, CO and NO reversibly at the haem iron, serves as a model for studying structural and dynamic aspects of protein reactions. Time-resolved spectroscopic measurements after photodissociation of the ligand revealed a complex ligand-binding reaction with multiple kinetic intermediates, resulting from protein relaxation and movements of the ligand within the protein. To observe the structural changes induced by ligand dissociation, we have carried out X-ray crystallographic investigations of carbon monoxy-myoglobin (MbCO mutant L29W) crystals illuminated below and above 180 K, complemented by time-resolved infrared spectroscopy of CO rebinding. Here we show that below 180 K photodissociated ligands migrate to specific sites within an internal cavity--the distal haem pocket--of an essentially immobilized, frozen protein, from where they subsequently rebind by thermally activated barrier crossing. Upon photodissociation above 180 K, ligands escape from the distal pocket, aided by protein fluctuations that transiently open exit channels. We recover most of the ligands in a cavity on the opposite side of the haem group.
-==Overview==
+Ligand binding and conformational motions in myoglobin.,Ostermann A, Waschipky R, Parak FG, Nienhaus GU Nature. 2000 Mar 9;404(6774):205-8. PMID:10724176<ref>PMID:10724176</ref>
-Myoglobin, a small globular haem protein that binds gaseous ligands such as O2, CO and NO reversibly at the haem iron, serves as a model for studying structural and dynamic aspects of protein reactions. Time-resolved spectroscopic measurements after photodissociation of the ligand revealed a complex ligand-binding reaction with multiple kinetic intermediates, resulting from protein relaxation and movements of the ligand within the protein. To observe the structural changes induced by ligand dissociation, we have carried out X-ray crystallographic investigations of carbon monoxy-myoglobin (MbCO mutant L29W) crystals illuminated below and above 180 K, complemented by time-resolved infrared spectroscopy of CO rebinding. Here we show that below 180 K photodissociated ligands migrate to specific sites within an internal cavity--the distal haem pocket--of an essentially immobilized, frozen protein, from where they subsequently rebind by thermally activated barrier crossing. Upon photodissociation above 180 K, ligands escape from the distal pocket, aided by protein fluctuations that transiently open exit channels. We recover most of the ligands in a cavity on the opposite side of the haem group.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-DO7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DO7 OCA].
+</div>
+<div class="pdbe-citations 1do7" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Ligand binding and conformational motions in myoglobin., Ostermann A, Waschipky R, Parak FG, Nienhaus GU, Nature. 2000 Mar 9;404(6774):205-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10724176 10724176]
+*[[Myoglobin 3D structures|Myoglobin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Physeter catodon]]
-[[Category: Single protein]]
+[[Category: Nienhaus GU]]
-[[Category: Nienhaus, G U.]]
+[[Category: Ostermann A]]
-[[Category: Ostermann, A.]]
+[[Category: Parak FG]]
-[[Category: Parak, F G.]]
+[[Category: Waschipky R]]
-[[Category: Waschipky, R.]]
-[[Category: Heme]]
-[[Category: Ligand migration]]
-[[Category: Photolysed myoglobin]]
-[[Category: Respiratory protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 14:04:34 2008''