1a3d: Difference between revisions

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-[[Image:1a3d.jpg|left|200px]]<br /><applet load="1a3d" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1a3d, resolution 1.8&Aring;" />
-'''PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM'''<br />
-==Overview==
+==PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM==
-Three crystal forms of Naja naja naja phospholipase A2 were discovered, through random crystallization screening, including two heretofore, uncharacterized forms. The crystallization conditions for both of these, novel crystal forms are Ca(2+)-free whereas previously reported conditions, include Ca2+. One of the new crystal forms has a cubic lattice in the, space group P2(1)3 (a = b = c = 69.24 A), the other has an orthorhombic, lattice in the space group P2(1)2(1)2(1) (a = 67.22 A, b = 73.48 A, c =, 87.52 A) and a previously characterized crystal belong to the tetragonal, space group P4(3)2(1)2 (a = b = 88.6 A, c = 107.4 A). The structure from, the cubic crystal form has been determined to 1.8 A and refined to an, R-factor of 17% while the structure from the orthorhombic form has been, determined to 2.65 A and has been refined to an R-factor of 21%. The, determination of the cubic structure extends the resolution to which, structures of this molecule have been determined from 2.3 A to 1.8 A. The, two newly determined structures, in combination with the previously, determined structure, generate an informative structural ensemble from, which structural changes due to Ca2+, which is required for catalysis, and, the effect of crystal contacts on side-chain conformations and oligomeric, association can be inferred. Both of the newly determined structures, reveal a trimeric oligomer as observed in the tetragonal structure; this, appears to be a unique feature of the Naja naja naja enzyme.
+<StructureSection load='1a3d' size='340' side='right'caption='[[1a3d]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1a3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_naja Naja naja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A3D 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=1a3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a3d OCA], [https://pdbe.org/1a3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a3d RCSB], [https://www.ebi.ac.uk/pdbsum/1a3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a3d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PA2A2_NAJNA PA2A2_NAJNA] PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
+== 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/a3/1a3d_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=1a3d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Three crystal forms of Naja naja naja phospholipase A2 were discovered through random crystallization screening, including two heretofore uncharacterized forms. The crystallization conditions for both of these novel crystal forms are Ca(2+)-free whereas previously reported conditions include Ca2+. One of the new crystal forms has a cubic lattice in the space group P2(1)3 (a = b = c = 69.24 A), the other has an orthorhombic lattice in the space group P2(1)2(1)2(1) (a = 67.22 A, b = 73.48 A, c = 87.52 A) and a previously characterized crystal belong to the tetragonal space group P4(3)2(1)2 (a = b = 88.6 A, c = 107.4 A). The structure from the cubic crystal form has been determined to 1.8 A and refined to an R-factor of 17% while the structure from the orthorhombic form has been determined to 2.65 A and has been refined to an R-factor of 21%. The determination of the cubic structure extends the resolution to which structures of this molecule have been determined from 2.3 A to 1.8 A. The two newly determined structures, in combination with the previously determined structure, generate an informative structural ensemble from which structural changes due to Ca2+, which is required for catalysis, and the effect of crystal contacts on side-chain conformations and oligomeric association can be inferred. Both of the newly determined structures reveal a trimeric oligomer as observed in the tetragonal structure; this appears to be a unique feature of the Naja naja naja enzyme.
-==About this Structure==
+Structures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing.,Segelke BW, Nguyen D, Chee R, Xuong NH, Dennis EA J Mol Biol. 1998 May 29;279(1):223-32. PMID:9636712<ref>PMID:9636712</ref>
-A3D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Naja_naja Naja naja] with NA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] Known structural/functional Site: <scene name='pdbsite=CAB:Ca Binding Residues'>CAB</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1A3D OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structures of two novel crystal forms of Naja naja naja phospholipase A2 lacking Ca2+ reveal trimeric packing., Segelke BW, Nguyen D, Chee R, Xuong NH, Dennis EA, J Mol Biol. 1998 May 29;279(1):223-32. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9636712 9636712]
+</div>
+<div class="pdbe-citations 1a3d" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phospholipase A2 3D structures|Phospholipase A2 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Naja naja]]
-[[Category: Phospholipase A(2)]]
+[[Category: Chee R]]
-[[Category: Single protein]]
+[[Category: Dennis EA]]
-[[Category: Chee, R.]]
+[[Category: Nguyen D]]
-[[Category: Dennis, E.A.]]
+[[Category: Segelke BW]]
-[[Category: Nguyen, D.]]
+[[Category: Xuong HN]]
-[[Category: Segelke, B.W.]]
-[[Category: Xuong, H.N.]]
-[[Category: NA]]
-[[Category: activator site]]
-[[Category: calcium binding]]
-[[Category: carboxylic ester hydrolase]]
-[[Category: phospholipase]]
-[[Category: trimer]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 14:08:17 2007''