1vbr: Difference between revisions

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-{{Seed}}
-[[Image:1vbr.png|left|200px]]
-<!--
+==Crystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose==
-The line below this paragraph, containing "STRUCTURE_1vbr", creates the "Structure Box" on the page.
+<StructureSection load='1vbr' size='340' side='right'caption='[[1vbr]], [[Resolution|resolution]] 1.80&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'>[[1vbr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBR 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-{{STRUCTURE_1vbr|  PDB=1vbr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbr OCA], [https://pdbe.org/1vbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vbr RCSB], [https://www.ebi.ac.uk/pdbsum/1vbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9WXS5_THEMA Q9WXS5_THEMA]
+== 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/vb/1vbr_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=1vbr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.
-===Crystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose===
+Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.,Ihsanawati, Kumasaka T, Kaneko T, Morokuma C, Yatsunami R, Sato T, Nakamura S, Tanaka N Proteins. 2005 Dec 1;61(4):999-1009. PMID:16247799<ref>PMID:16247799</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16247799}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1vbr" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16247799 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16247799}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VBR is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBR OCA].
-==Reference==
-<ref group="xtra">PMID:16247799</ref><ref group="xtra">PMID:12925805</ref><references group="xtra"/>
-[[Category: Endo-1,4-beta-xylanase]]
 [[Category: Thermotoga maritima]]
 [[Category: Ihsanawati]]
-[[Category: Kaneko, T.]]
+[[Category: Kaneko T]]
-[[Category: Kumasaka, T.]]
+[[Category: Kumasaka T]]
-[[Category: Nakamura, S.]]
+[[Category: Nakamura S]]
-[[Category: Tanaka, N.]]
+[[Category: Tanaka N]]
-[[Category: Xylanase 10b]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:23:55 2009''