1m7s: 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: @@
 ==Crystal Structure Analysis of Catalase CatF of Pseudomonas syringae==
-<StructureSection load='1m7s' size='340' side='right' caption='[[1m7s]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='1m7s' size='340' side='right'caption='[[1m7s]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1m7s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19310 Atcc 19310]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1m7s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_syringae Pseudomonas syringae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M7S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CATF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=317 ATCC 19310])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></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=1m7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7s OCA], [https://pdbe.org/1m7s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m7s RCSB], [https://www.ebi.ac.uk/pdbsum/1m7s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7s ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m7s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7s OCA], [http://pdbe.org/1m7s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m7s RCSB], [http://www.ebi.ac.uk/pdbsum/1m7s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7s ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CATB_PSESY CATB_PSESY]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
+[https://www.uniprot.org/uniprot/CATB_PSESY CATB_PSESY] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
 == 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/m7/1m7s_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m7/1m7s_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / Line 20: @@
 </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=1m7s ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Catalase CatF of Pseudomonas syringae has been identified phylogenetically as a clade 1 catalase, closely related to plant catalases, a group from which no structure has been determined. The structure of CatF has been refined at 1.8 A resolution by using X-ray synchrotron data collected from a crystal flash-cooled with liquid nitrogen. The crystallographic agreement factors R and R(free) are, respectively, 18.3% and 24.0%. The asymmetric unit of the crystal contains a whole molecule that shows accurate 222-point group symmetry. The crystallized enzyme is a homotetramer of subunits with 484 residues, some 26 residues shorter than predicted from the DNA sequence. Mass spectrometry analysis confirmed the absence of 26 N-terminal residues, possibly removed by a periplasmic transport system. The core structure of the CatF subunit was closely related to seven other catalases with root-mean-square deviations (RMSDs) of 368 core Calpha atoms of 0.99-1.30 A. The heme component of CatF is heme b in the same orientation that is found in Escherichia coli hydroperoxidase II, an orientation that is flipped 180 degrees with respect the orientation of the heme in bovine liver catalase. NADPH is not found in the structure of CatF because key residues required for nucleotide binding are missing; 2129 water molecules were refined into the model. Water occupancy in the main or perpendicular channel of CatF varied among the four subunits from two to five in the region between the heme and the conserved Asp150. A comparison of the water occupancy in this region with the same region in other catalases reveals significant differences among the catalases.
-Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution.,Carpena X, Soriano M, Klotz MG, Duckworth HW, Donald LJ, Melik-Adamyan W, Fita I, Loewen PC Proteins. 2003 Feb 15;50(3):423-36. PMID:12557185<ref>PMID:12557185</ref>
+==See Also==
+*[[Catalase 3D structures|Catalase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1m7s" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 19310]]
+[[Category: Large Structures]]
-[[Category: Catalase]]
+[[Category: Pseudomonas syringae]]
-[[Category: Carpena, X]]
+[[Category: Carpena X]]
-[[Category: Donald, L J]]
+[[Category: Donald LJ]]
-[[Category: Duckworth, H W]]
+[[Category: Duckworth HW]]
-[[Category: Fita, I]]
+[[Category: Fita I]]
-[[Category: Klotz, M G]]
+[[Category: Klotz MG]]
-[[Category: Loewen, P C]]
+[[Category: Loewen PC]]
-[[Category: Melik-Adamyan, W]]
+[[Category: Melik-Adamyan W]]
-[[Category: Soriano, M]]
+[[Category: Soriano M]]
-[[Category: Alpha helical domain]]
-[[Category: Beta barrel]]
-[[Category: Oxidoreductase]]