1f5j: Difference between revisions

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1f5j.jpg|left|200px]]<br /><applet load="1f5j" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1f5j, resolution 1.80&Aring;" />
-'''CRYSTAL STRUCTURE OF XYNB, A HIGHLY THERMOSTABLE BETA-1,4-XYLANASE FROM DICTYOGLOMUS THERMOPHILUM RT46B.1, AT 1.8 A RESOLUTION'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF XYNB, A HIGHLY THERMOSTABLE BETA-1,4-XYLANASE FROM DICTYOGLOMUS THERMOPHILUM RT46B.1, AT 1.8 A RESOLUTION==
-Microorganisms employ a large array of enzymes to break down the cellulose, and hemicelluloses of plant biomass. These enzymes, especially those with, high thermal stability, have many uses in biotechnology. We have solved, the crystal structure of a beta-1, 4-xylanase, XynB, from the extremely, thermophilic bacterium Dictyoglomus thermophilum, isolate Rt46B.1. The, protein crystallized from 1.6 M ammonium sulfate, 0.2 M HEPES pH 7.2 and, 10% glycerol, with unit-cell parameters a = b = 91.3, c = 44.9 A and space, group P4(3). The structure was solved at high resolution (1.8 A) by X-ray, crystallography, using the method of isomorphous replacement with a single, mercury derivative, and refined to a final R factor of 18.3% (R(free) =, 22.1%). XynB has the single-domain fold typical of family 11 xylanases, comprising a jelly roll of two highly twisted beta-sheets that create a, deep substrate-binding cleft. The two catalytic residues, Glu90 and, Glu180, occupy this cleft. Compared with other family 11 xylanases, XynB, has a greater proportion of polar surface and has a slightly extended, C-terminus that, combined with the extension of beta-strand A5, gives, additional hydrogen bonding and hydrophobic packing. These factors may, account for the enhanced thermal stability of the enzyme.
+<StructureSection load='1f5j' size='340' side='right'caption='[[1f5j]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1f5j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyoglomus_thermophilum Dictyoglomus thermophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F5J FirstGlance]. <br>
-F5J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Dictyoglomus_thermophilum Dictyoglomus thermophilum] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1F5J OCA].
+</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5j OCA], [https://pdbe.org/1f5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f5j RCSB], [https://www.ebi.ac.uk/pdbsum/1f5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5j ProSAT]</span></td></tr>
-Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution., McCarthy AA, Morris DD, Bergquist PL, Baker EN, Acta Crystallogr D Biol Crystallogr. 2000 Nov;56(Pt 11):1367-75. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11053833 11053833]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/P77853_DICTH P77853_DICTH]
+== 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/f5/1f5j_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=1f5j ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Dictyoglomus thermophilum]]
-[[Category: Endo-1,4-beta-xylanase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Baker EN]]
-[[Category: Baker, E.N.]]
+[[Category: McCarthy AA]]
-[[Category: McCarthy, A.A.]]
-[[Category: SO4]]
-[[Category: beta-barrel]]
-[[Category: xylanase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:19:12 2007''