1r76: Difference between revisions

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-[[Image:1r76.jpg|left|200px]]
-<!--
+==Structure of a pectate lyase from Azospirillum irakense==
-The line below this paragraph, containing "STRUCTURE_1r76", creates the "Structure Box" on the page.
+<StructureSection load='1r76' size='340' side='right'caption='[[1r76]], [[Resolution|resolution]] 2.65&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'>[[1r76]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Niveispirillum_irakense Niveispirillum irakense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R76 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R76 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]] 2.65&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
-{{STRUCTURE_1r76|  PDB=1r76  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r76 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r76 OCA], [https://pdbe.org/1r76 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r76 RCSB], [https://www.ebi.ac.uk/pdbsum/1r76 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r76 ProSAT]</span></td></tr>
+</table>
-'''Structure of a pectate lyase from Azospirillum irakense'''
+== Function ==
+[https://www.uniprot.org/uniprot/Q9X592_NIVIR Q9X592_NIVIR]
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-The three-dimensional structure of Azospirillum irakense pectate lyase (PelA) has been determined at a resolution of 2.65 A. The crystals are hexagonal, belonging to space group P6(5)22, with unit-cell parameters a = b = 85.37, c = 231.32 angstroms. Phase information was derived from a multiple-wavelength anomalous dispersion (MAD) experiment using a Hg derivative. Refinement of the model converged to Rcryst = 20.08% and Rfree = 25.87%. The overall structure of PelA does not adopt the characteristic parallel beta-helix fold displayed by pectate lyases from polysaccharide lyase (PL) families PL1, PL3 and PL9. Instead, it displays a predominantly alpha-helical structure with irregular coils and short beta-strands, similar to the recently reported structure of the catalytic module of the Cellvibrio japonicus pectate lyase Pel10Acm. The topologies of the two structures have been compared. They show two 'domains' with the interface between them being a wide-open central groove in which the active site is located. The active sites of the crystal structures are also compared and their similarities and differences are discussed.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/1r76_consurf.spt"</scriptWhenChecked>
-R76 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Azospirillum_irakense Azospirillum irakense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R76 OCA].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-Azospirillum irakense pectate lyase displays a toroidal fold., Novoa De Armas H, Verboven C, De Ranter C, Desair J, Vande Broek A, Vanderleyden J, Rabijns A, Acta Crystallogr D Biol Crystallogr. 2004 Jun;60(Pt 6):999-1007. Epub 2004, May 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15159558 15159558]
+</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=1r76 ConSurf].
-[[Category: Azospirillum irakense]]
+<div style="clear:both"></div>
-[[Category: Pectate lyase]]
+__TOC__
-[[Category: Single protein]]
+</StructureSection>
-[[Category: Armas, H Novoa de.]]
+[[Category: Large Structures]]
-[[Category: Broek, A Vande.]]
+[[Category: Niveispirillum irakense]]
-[[Category: Desair, J.]]
+[[Category: De Ranter C]]
-[[Category: Rabijns, A.]]
+[[Category: Desair J]]
-[[Category: Ranter, C De.]]
+[[Category: Novoa de Armas H]]
-[[Category: Vanderleyden, J.]]
+[[Category: Rabijns A]]
-[[Category: Verboven, C.]]
+[[Category: Vande Broek A]]
-[[Category: A-helical structure]]
+[[Category: Vanderleyden J]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 07:10:02 2008''
+[[Category: Verboven C]]