3odd: Difference between revisions

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-{{Seed}}
-[[Image:3odd.jpg|left|200px]]
-<!--
+==Comparison of the character and the speed of X-ray-induced structural changes of porcine pancreatic elastase at two temperatures, 100 and 15K. The data set was collected from region B of the crystal. Second step of radiation damage==
-The line below this paragraph, containing "STRUCTURE_3odd", creates the "Structure Box" on the page.
+<StructureSection load='3odd' size='340' side='right'caption='[[3odd]], [[Resolution|resolution]] 1.10&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'>[[3odd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ODD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ODD 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]] 1.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3odd|  PDB=3odd  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3odd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3odd OCA], [https://pdbe.org/3odd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3odd RCSB], [https://www.ebi.ac.uk/pdbsum/3odd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3odd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CELA1_PIG CELA1_PIG] Acts upon elastin.
+== 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/od/3odd_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=3odd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Overall and site-specific X-ray-induced damage to porcine pancreatic elastase was studied at atomic resolution at temperatures of 100 and 15 K. The experiments confirmed that irradiation causes small movements of protein domains and bound water molecules in protein crystals. These structural changes occur not only at 100 K but also at temperatures as low as 15 K. An investigation of the deterioration of disulfide bridges demonstrated the following. (i) A decrease in the occupancy of S(gamma) atoms and the appearance of new cysteine rotamers occur simultaneously. (ii) The occupancy decrease is observed for all S(gamma) atoms, while new rotamers arise for some of the cysteine residues; the appearance of new conformations correlates with the accessibility to solvent. (iii) The sum of the occupancies of the initial and new conformations of a cysteine residue is approximately equal to the occupancy of the second cysteine residue in the bridge. (iv) The most pronounced changes occur at doses below 1.4 x 10(7) Gy, with only small changes occurring at higher doses. Comparison of the radiation-induced changes in an elastase crystal at 100 and 15 K suggested that the dose needed to induce a similar level of deterioration of the disulfide bonds and atomic displacements at 15 K to those seen at 100 K is more than two times higher.
-===Comparison of the character and the speed of X-ray-induced structural changes of porcine pancreatic elastase at two temperatures, 100 and 15K. The data set was collected from region B of the crystal. Second step of radiation damage===
+X-ray-induced deterioration of disulfide bridges at atomic resolution.,Petrova T, Ginell S, Mitschler A, Kim Y, Lunin VY, Joachimiak G, Cousido-Siah A, Hazemann I, Podjarny A, Lazarski K, Joachimiak A Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1075-91. Epub 2010, Sep 18. PMID:20944241<ref>PMID:20944241</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3odd" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-ODD is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ODD OCA].
+*[[Elastase 3D structures|Elastase 3D structures]]
-[[Category: Pancreatic elastase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Sus scrofa]]
-[[Category: Cousido-Siah, A.]]
+[[Category: Cousido-Siah A]]
-[[Category: Ginell, S.]]
+[[Category: Ginell S]]
-[[Category: Hazemann, I.]]
+[[Category: Hazemann I]]
-[[Category: Joachimiak, A.]]
+[[Category: Joachimiak A]]
-[[Category: Mitschler, A.]]
+[[Category: Mitschler A]]
-[[Category: Petrova, T.]]
+[[Category: Petrova T]]
-[[Category: Podjarny, A.]]
+[[Category: Podjarny A]]
-[[Category: Atomic resolution]]
-[[Category: Disulfide bridge]]
-[[Category: Hydrolase]]
-[[Category: Radiation damage]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 09:03:55 2010''