1gox: Difference between revisions

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-[[Image:1gox.jpg|left|200px]]<br /><applet load="1gox" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1gox, resolution 2.0&Aring;" />
-'''REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION'''<br />
-==Overview==
+==REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION==
-The amino acid sequence of glycolate oxidase from spinach has been fitted, to an electron density map of 2.0 A nominal resolution and the structure, has been refined using the restrained parameter least-squares refinement, of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was, obtained for 32,888 independent reflections from 5.5 to 2 A resolution., The geometry of the model, consisting of 350 amino acid residues, the, cofactor flavin mononucleotide and 298 solvent molecules, is close to, ideal with root-mean-square deviations of 0.015 A in bond lengths and 2.6, degrees in bond angles. The expected trimodal distribution with preference, for staggered conformation is obtained for the side-chain chi 1-angles., The core of the subunit is built up from the eight beta-strands in the, beta/alpha-barrel. This core consists of two hydrophobic layers. One in, the center is made up of residues pointing in from the beta-strands, towards the barrel axis and the second, consisting of two segments of, residues, pointing out from the beta-strands towards the eight, alpha-helices of the barrel and pointing from the helices towards the, strands. The hydrogen bond pattern for the beta-strands in the, beta/alpha-barrel is described. There are a number of residues with, 3(10)-helix conformation, in particular there is one left-handed helix., The ordered solvent molecules are organized mainly in clusters. The, average isotropic temperature factor is quite high, 27.1 A2, perhaps a, reflection of the high solvent content in the crystal. The octameric, glycolate oxidase molecule, which has 422 symmetry, makes strong, interactions around the 4-fold axis forming a tight tetramer, but only, weak interactions between the two tetramers forming the octamer.
+<StructureSection load='1gox' size='340' side='right'caption='[[1gox]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1gox]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GOX 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=1gox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gox OCA], [https://pdbe.org/1gox PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gox RCSB], [https://www.ebi.ac.uk/pdbsum/1gox PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gox ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GOX_SPIOL GOX_SPIOL]
+== 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/go/1gox_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=1gox ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The amino acid sequence of glycolate oxidase from spinach has been fitted to an electron density map of 2.0 A nominal resolution and the structure has been refined using the restrained parameter least-squares refinement of Hendrickson and Konnert. A final crystallographic R-factor of 18.9% was obtained for 32,888 independent reflections from 5.5 to 2 A resolution. The geometry of the model, consisting of 350 amino acid residues, the cofactor flavin mononucleotide and 298 solvent molecules, is close to ideal with root-mean-square deviations of 0.015 A in bond lengths and 2.6 degrees in bond angles. The expected trimodal distribution with preference for staggered conformation is obtained for the side-chain chi 1-angles. The core of the subunit is built up from the eight beta-strands in the beta/alpha-barrel. This core consists of two hydrophobic layers. One in the center is made up of residues pointing in from the beta-strands towards the barrel axis and the second, consisting of two segments of residues, pointing out from the beta-strands towards the eight alpha-helices of the barrel and pointing from the helices towards the strands. The hydrogen bond pattern for the beta-strands in the beta/alpha-barrel is described. There are a number of residues with 3(10)-helix conformation, in particular there is one left-handed helix. The ordered solvent molecules are organized mainly in clusters. The average isotropic temperature factor is quite high, 27.1 A2, perhaps a reflection of the high solvent content in the crystal. The octameric glycolate oxidase molecule, which has 422 symmetry, makes strong interactions around the 4-fold axis forming a tight tetramer, but only weak interactions between the two tetramers forming the octamer.
-==About this Structure==
+Refined structure of spinach glycolate oxidase at 2 A resolution.,Lindqvist Y J Mol Biol. 1989 Sep 5;209(1):151-66. PMID:2681790<ref>PMID:2681790</ref>
-GOX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea] with ACE and FMN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/(S)-2-hydroxy-acid_oxidase (S)-2-hydroxy-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.15 1.1.3.15] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GOX OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Refined structure of spinach glycolate oxidase at 2 A resolution., Lindqvist Y, J Mol Biol. 1989 Sep 5;209(1):151-66. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2681790 2681790]
+</div>
-[[Category: (S)-2-hydroxy-acid oxidase]]
+<div class="pdbe-citations 1gox" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+==See Also==
+*[[Glycolate oxidase 3D structures|Glycolate oxidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Spinacia oleracea]]
-[[Category: Lindqvist, Y.]]
+[[Category: Lindqvist Y]]
-[[Category: ACE]]
-[[Category: FMN]]
-[[Category: oxidoreductase (oxygen(a))]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 16:12:40 2007''