1qaz: Difference between revisions

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<StructureSection load='1qaz' size='340' side='right'caption='[[1qaz]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
<StructureSection load='1qaz' size='340' side='right'caption='[[1qaz]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1qaz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'rhizomonas'_sp. 'rhizomonas' sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QAZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QAZ FirstGlance]. <br>
<table><tr><td colspan='2'>[[1qaz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp. Sphingomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QAZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QAZ FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Urea_carboxylase Urea carboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.6 6.3.4.6] </span></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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qaz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qaz OCA], [https://pdbe.org/1qaz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qaz RCSB], [https://www.ebi.ac.uk/pdbsum/1qaz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qaz ProSAT]</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=1qaz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qaz OCA], [https://pdbe.org/1qaz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qaz RCSB], [https://www.ebi.ac.uk/pdbsum/1qaz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qaz ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9KWU1_SPHSX Q9KWU1_SPHSX]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1qaz ConSurf].
</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=1qaz ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional structure of alginate lyase A1-III (ALYIII) from a Sphingomonas species A1 was determined by X-ray crystallography. The enzyme was crystallized by the hanging-drop vapour-diffusion method in the presence of 49% ammonium sulfate at 20 degrees C. The crystals are monoclinic and belong to the space group C2 with unit cell dimensions of a=49.18 A, b=93.08 A, c=82.10 A and beta=104.12 degrees. There was one molecule of alginate lyase in the asymmetric unit of the crystal. The diffraction data up to 1. 71 A were collected with Rsymof 5.0%. The crystal structure of ALYIII was solved by the multiple isomorphous replacement method and refined at 1.78 A resolution using X-PLOR with a final R -factor of 18.0% for 10.0 to 1.78 A resolution data. The refined model of ALYIII contained 351 amino acid residues, 299 water molecules and two sulfate ions. The three-dimensional structure of ALYIII was abundant in helices and had a deep tunnel-like cleft in a novel (alpha6/alpha5)-barrel structure, which was similar to the (alpha6/alpha6)-barrel found in glucoamylase and cellulase. This structure presented the possibility that alginate molecules might penetrate into the cleft to interact with the catalytic site of ALYIII.
Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.,Yoon HJ, Mikami B, Hashimoto W, Murata K J Mol Biol. 1999 Jul 9;290(2):505-14. PMID:10390348<ref>PMID:10390348</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1qaz" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Rhizomonas sp]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Urea carboxylase]]
[[Category: Sphingomonas sp]]
[[Category: Yoon, H J]]
[[Category: Yoon H-J]]
[[Category: Alginate lyase]]
[[Category: Crystal]]
[[Category: Lyase]]
Retrieved from "https://proteopedia.org/1qaz"