2duu: Difference between revisions

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-[[Image:2duu.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2duu", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2duu|  PDB=2duu  |  SCENE=  }}
-'''Crystal Structure of apo-form of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp.'''
+==Crystal Structure of apo-form of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp.==
+<StructureSection load='2duu' size='340' side='right'caption='[[2duu]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2duu]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_7942_=_FACHB-805 Synechococcus elongatus PCC 7942 = FACHB-805]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DUU 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]] 2.9&#8491;</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=2duu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2duu OCA], [https://pdbe.org/2duu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2duu RCSB], [https://www.ebi.ac.uk/pdbsum/2duu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2duu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9R6W2_SYNE7 Q9R6W2_SYNE7]
+== 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/du/2duu_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2duu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of NADP-dependent apo-glyceraldehyde-3-phosphate dehydrogenase (apo-GAPDH) from Synechococcus PCC 7942 is reported. The crystal structure was solved by molecular replacement and refined to an R of 21.7% and R(free) of 27.5% at 2.9 angstroms resolution. The structural features of apo-GAPDH are as follows. The S-loop has an extremely flexible conformation and the sulfate ion is only taken into the classical P(i) site. A structural comparison with holo-GAPDHs indicated that the S-loop fixation is essential in the discrimination of NADP and NAD molecules.
-==Overview==
+Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942.,Kitatani T, Nakamura Y, Wada K, Kinoshita T, Tamoi M, Shigeoka S, Tada T Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Aug 1;62(Pt, 8):727-30. Epub 2006 Jul 29. PMID:16880542<ref>PMID:16880542</ref>
-The crystal structure of NADP-dependent apo-glyceraldehyde-3-phosphate dehydrogenase (apo-GAPDH) from Synechococcus PCC 7942 is reported. The crystal structure was solved by molecular replacement and refined to an R of 21.7% and R(free) of 27.5% at 2.9 angstroms resolution. The structural features of apo-GAPDH are as follows. The S-loop has an extremely flexible conformation and the sulfate ion is only taken into the classical P(i) site. A structural comparison with holo-GAPDHs indicated that the S-loop fixation is essential in the discrimination of NADP and NAD molecules.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-DUU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DUU OCA].
+</div>
+<div class="pdbe-citations 2duu" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942., Kitatani T, Nakamura Y, Wada K, Kinoshita T, Tamoi M, Shigeoka S, Tada T, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Aug 1;62(Pt, 8):727-30. Epub 2006 Jul 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16880542 16880542]
+*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
-[[Category: Single protein]]
+== References ==
-[[Category: Synechococcus sp.]]
+<references/>
-[[Category: Kinoshita, T.]]
+__TOC__
-[[Category: Kitatani, T.]]
+</StructureSection>
-[[Category: Nakamura, Y.]]
+[[Category: Large Structures]]
-[[Category: Shigeoka, S.]]
+[[Category: Synechococcus elongatus PCC 7942 = FACHB-805]]
-[[Category: Tada, T.]]
+[[Category: Kinoshita T]]
-[[Category: Tamoi, M.]]
+[[Category: Kitatani T]]
-[[Category: Wada, K.]]
+[[Category: Nakamura Y]]
-[[Category: Apo-form]]
+[[Category: Shigeoka S]]
-[[Category: Glyceraldehyde 3-phosphate dehydrogenase]]
+[[Category: Tada T]]
-[[Category: Rossmann fold]]
+[[Category: Tamoi M]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 01:25:20 2008''
+[[Category: Wada K]]