2ze9: 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:2ze9.jpg|left|200px]]<br /><applet load="2ze9" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2ze9, resolution 2.30&Aring;" />
-'''Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine'''<br />
-==Overview==
+==Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine==
-Phospholipase D (E.C. 3.1.4.4) from Streptomyces antibioticus has been, crystallized in six crystal forms using the hanging-drop vapour-diffusion, method. The type III and V crystals belong to monoclinic and hexagonal, systems, respectively. All of the other crystal forms, types I, II, IV and, VI, belong to orthorhombic space group P212121. Of these four types, the, type VI crystals are suitable for X-ray structure determination. Crystal, data for type VI crystals are: a = 50.1, b = 98.7, c = 107.6 A, V = 532100, A3, Z = 4 and Vm = 2.47 A3 Da-1. Type VI crystals diffract to at least 2.3, A resolution. A total of 11295 independent reflections to 3 A resolution, have been collected from a type VI crystal using a conventional X-ray, source, and its structural analysis is currently being conducted using, isomorphous replacement methods.
+<StructureSection load='2ze9' size='340' side='right'caption='[[2ze9]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ze9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZE9 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PD7:(2R)-3-(PHOSPHONOOXY)PROPANE-1,2-DIYL+DIHEPTANOATE'>PD7</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=2ze9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ze9 OCA], [https://pdbe.org/2ze9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ze9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ze9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ze9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PLD_STRAT PLD_STRAT]
+== 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/ze/2ze9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2ze9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phospholipase D (E.C. 3.1.4.4) from Streptomyces antibioticus has been crystallized in six crystal forms using the hanging-drop vapour-diffusion method. The type III and V crystals belong to monoclinic and hexagonal systems, respectively. All of the other crystal forms, types I, II, IV and VI, belong to orthorhombic space group P212121. Of these four types, the type VI crystals are suitable for X-ray structure determination. Crystal data for type VI crystals are: a = 50.1, b = 98.7, c = 107.6 A, V = 532100 A3, Z = 4 and Vm = 2.47 A3 Da-1. Type VI crystals diffract to at least 2.3 A resolution. A total of 11295 independent reflections to 3 A resolution have been collected from a type VI crystal using a conventional X-ray source, and its structural analysis is currently being conducted using isomorphous replacement methods.
-==About this Structure==
+Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus.,Suzuki A, Kakuno K, Iwasaki Y, Yamane T, Yamane T Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):317-9. Epub 1999, Jan 1. PMID:010089437<ref>PMID:010089437</ref>
-ZE9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus] with <scene name='pdbligand=MES:'>MES</scene> and <scene name='pdbligand=PD7:'>PD7</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phospholipase_D Phospholipase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.4 3.1.4.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZE9 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus., Suzuki A, Kakuno K, Iwasaki Y, Yamane T, Yamane T, Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):317-9. Epub 1999, Jan 1. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10089437 10089437]
+</div>
-[[Category: Phospholipase D]]
+<div class="pdbe-citations 2ze9" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+==See Also==
+*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces antibioticus]]
-[[Category: Iwasaki, Y.]]
+[[Category: Iwasaki Y]]
-[[Category: Suzuki, A.]]
+[[Category: Suzuki A]]
-[[Category: Toda, H.]]
+[[Category: Toda H]]
-[[Category: Yamane, T.]]
+[[Category: Yamane T]]
-[[Category: MES]]
-[[Category: PD7]]
-[[Category: alpha-beta-beta-alpha sandwich]]
-[[Category: hydrolase]]
-[[Category: lipid degradation]]
-[[Category: secreted]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:29:26 2008''