2oe9: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2oe9.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2oe9", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2oe9|  PDB=2oe9  |  SCENE=  }}
-'''High-pressure structure of pseudo-WT T4 Lysozyme'''
+==High-pressure structure of pseudo-WT T4 Lysozyme==
+<StructureSection load='2oe9' size='340' side='right'caption='[[2oe9]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2oe9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OE9 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]] 2.01&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=2oe9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oe9 OCA], [https://pdbe.org/2oe9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oe9 RCSB], [https://www.ebi.ac.uk/pdbsum/2oe9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oe9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
+== 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/oe/2oe9_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=2oe9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Steric constraints, charged interactions and many other forces important to protein structure and function can be explored by mutagenic experiments. Research of this kind has led to a wealth of knowledge about what stabilizes proteins in their folded states. To gain a more complete picture requires that we perturb these structures in a continuous manner, something mutagenesis cannot achieve. With high pressure crystallographic methods it is now possible to explore the detailed properties of proteins while continuously varying thermodynamic parameters. Here, we detail the structural response of the cavity-containing mutant L99A of T4 lysozyme, as well as its pseudo wild-type (WT*) counterpart, to hydrostatic pressure. Surprisingly, the cavity has almost no effect on the pressure response: virtually the same changes are observed in WT* as in L99A under pressure. The cavity is most rigid, while other regions deform substantially. This implies that while some residues may increase the thermodynamic stability of a protein, they may also be structurally irrelevant. As recently shown, the cavity fills with water at pressures above 100 MPa while retaining its overall size. The resultant picture of the protein is one in which conformationally fluctuating side groups provide a liquid-like environment, but which also contribute to the rigidity of the peptide backbone.
-==Overview==
+Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography.,Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM J Mol Biol. 2007 Mar 30;367(3):752-63. Epub 2006 Dec 15. PMID:17292912<ref>PMID:17292912</ref>
-Steric constraints, charged interactions and many other forces important to protein structure and function can be explored by mutagenic experiments. Research of this kind has led to a wealth of knowledge about what stabilizes proteins in their folded states. To gain a more complete picture requires that we perturb these structures in a continuous manner, something mutagenesis cannot achieve. With high pressure crystallographic methods it is now possible to explore the detailed properties of proteins while continuously varying thermodynamic parameters. Here, we detail the structural response of the cavity-containing mutant L99A of T4 lysozyme, as well as its pseudo wild-type (WT*) counterpart, to hydrostatic pressure. Surprisingly, the cavity has almost no effect on the pressure response: virtually the same changes are observed in WT* as in L99A under pressure. The cavity is most rigid, while other regions deform substantially. This implies that while some residues may increase the thermodynamic stability of a protein, they may also be structurally irrelevant. As recently shown, the cavity fills with water at pressures above 100 MPa while retaining its overall size. The resultant picture of the protein is one in which conformationally fluctuating side groups provide a liquid-like environment, but which also contribute to the rigidity of the peptide backbone.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-OE9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OE9 OCA].
+</div>
+<div class="pdbe-citations 2oe9" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography., Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM, J Mol Biol. 2007 Mar 30;367(3):752-63. Epub 2006 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17292912 17292912]
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-[[Category: Enterobacteria phage t4]]
+== References ==
-[[Category: Lysozyme]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Collins, M D.]]
+</StructureSection>
-[[Category: Gruner, S M.]]
+[[Category: Escherichia virus T4]]
-[[Category: Matthews, B W.]]
+[[Category: Large Structures]]
-[[Category: Quillin, M L.]]
+[[Category: Collins MD]]
-[[Category: High-pressure]]
+[[Category: Gruner SM]]
-[[Category: T4 lysozyme]]
+[[Category: Matthews BW]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 10:43:42 2008''
+[[Category: Quillin ML]]