2ddx: Difference between revisions

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[[Image:2ddx.png|left|200px]]


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==Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4==
The line below this paragraph, containing "STRUCTURE_2ddx", creates the "Structure Box" on the page.
<StructureSection load='2ddx' size='340' side='right'caption='[[2ddx]], [[Resolution|resolution]] 0.86&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'>[[2ddx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_sp._AX-4 Vibrio sp. AX-4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DDX 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]] 0.86&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
{{STRUCTURE_2ddx|  PDB=2ddx  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ddx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ddx OCA], [https://pdbe.org/2ddx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ddx RCSB], [https://www.ebi.ac.uk/pdbsum/2ddx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ddx ProSAT]</span></td></tr>
 
</table>
===Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4===
== Function ==
 
[https://www.uniprot.org/uniprot/3XYN1_VIBSX 3XYN1_VIBSX] Catalyzes the hydrolysis of beta-1,3-xylan into oligosaccharides, mainly xylobiose, xylotriose and xylotetraose. Converts beta-1,3-xylotriose into xylose and xylobiose, converts beta-1,3-xylotetraose mainly into xylotriose and xylose, converts beta-1,3-xylopentaose into xylobiose and xylotriose. Does not hydrolyze beta-1,4-xylan, beta-1,4-mannan, beta-1,4-glucan, beta-1,3-xylobiose or p-nitrophenyl-beta-xyloside.<ref>PMID:15743273</ref>
 
== Evolutionary Conservation ==
==About this Structure==
[[Image:Consurf_key_small.gif|200px|right]]
2DDX is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_sp. Vibrio sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DDX OCA].  
Check<jmol>
[[Category: Vibrio sp.]]
  <jmolCheckbox>
[[Category: Sakaguchi, K.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2ddx_consurf.spt"</scriptWhenChecked>
[[Category: Beta-1,3-xylanase]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
[[Category: Glycoside hydrolase]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Tim barrel]]
  </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=2ddx ConSurf].
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:04:37 2009''
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Vibrio sp. AX-4]]
[[Category: Sakaguchi K]]

Latest revision as of 08:09, 17 October 2024

Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4

Structural highlights

2ddx is a 1 chain structure with sequence from Vibrio sp. AX-4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 0.86Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

3XYN1_VIBSX Catalyzes the hydrolysis of beta-1,3-xylan into oligosaccharides, mainly xylobiose, xylotriose and xylotetraose. Converts beta-1,3-xylotriose into xylose and xylobiose, converts beta-1,3-xylotetraose mainly into xylotriose and xylose, converts beta-1,3-xylopentaose into xylobiose and xylotriose. Does not hydrolyze beta-1,4-xylan, beta-1,4-mannan, beta-1,4-glucan, beta-1,3-xylobiose or p-nitrophenyl-beta-xyloside.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Kiyohara M, Sakaguchi K, Yamaguchi K, Araki T, Nakamura T, Ito M. Molecular cloning and characterization of a novel beta-1,3-xylanase possessing two putative carbohydrate-binding modules from a marine bacterium Vibrio sp. strain AX-4. Biochem J. 2005 Jun 15;388(Pt 3):949-57. PMID:15743273 doi:http://dx.doi.org/10.1042/BJ20050190

2ddx, resolution 0.86Å

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