3ixq: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3ixq.png|left|200px]]
-<!--
+==Structure of ribose 5-phosphate isomerase a from methanocaldococcus jannaschii==
-The line below this paragraph, containing "STRUCTURE_3ixq", creates the "Structure Box" on the page.
+<StructureSection load='3ixq' size='340' side='right'caption='[[3ixq]], [[Resolution|resolution]] 1.78&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'>[[3ixq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pjm 2pjm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IXQ 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]] 1.78&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PGO:S-1,2-PROPANEDIOL'>PGO</scene></td></tr>
-{{STRUCTURE_3ixq|  PDB=3ixq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ixq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixq OCA], [https://pdbe.org/3ixq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ixq RCSB], [https://www.ebi.ac.uk/pdbsum/3ixq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ixq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPIA_METJA RPIA_METJA]
+== 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/ix/3ixq_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=3ixq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribose-5-phosphate isomerase is a ubiquitous intracellular enzyme of bacterial, plant and animal origin that is involved in the pentose phosphate cycle, an essential component of cellular carbohydrate metabolism. Specifically, the enzyme catalyses the reversible conversion of ribose 5-phosphate to ribulose 5-phosphate. The structure of ribose-5-phosphate isomerase from Methanocaldococcus jannaschii has been solved in space group P2(1) to 1.78 A resolution using molecular replacement with one homotetramer in the asymmetric unit and refined to an R factor of 14.8%. The active site in each subunit was occupied by two molecules of propylene glycol in different orientations, one of which corresponds to the location of the phosphate moiety and the other to the location of the furanose ring of the inhibitor.
-===Structure of ribose 5-phosphate isomerase a from methanocaldococcus jannaschii===
+The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603).,Strange RW, Antonyuk SV, Ellis MJ, Bessho Y, Kuramitsu S, Yokoyama S, Hasnain SS Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Dec 1;65(Pt, 12):1214-7. Epub 2009 Nov 27. PMID:20054114<ref>PMID:20054114</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ixq" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20054114}}, adds the Publication Abstract to the page
+*[[Ribose-5-phosphate isomerase 3D structures|Ribose-5-phosphate isomerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20054114 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20054114}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-IXQ is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pjm 2pjm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXQ OCA].
-==Reference==
-<ref group="xtra">PMID:20054114</ref><references group="xtra"/>
 [[Category: Methanocaldococcus jannaschii]]
-[[Category: Ribose-5-phosphate isomerase]]
+[[Category: Antonyuk SV]]
-[[Category: Antonyuk, S V.]]
+[[Category: Bessho Y]]
-[[Category: Bessho, Y.]]
+[[Category: Ellis MJ]]
-[[Category: Ellis, M J.]]
+[[Category: Hasnain SS]]
-[[Category: Hasnain, S S.]]
+[[Category: Kuramitsu S]]
-[[Category: Kuramitsu, S.]]
+[[Category: Strange RW]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Yokoyama S]]
-[[Category: Strange, R W.]]
-[[Category: Yokoyama, S.]]
-[[Category: Carbohydrate metabolism]]
-[[Category: Carbon fixation]]
-[[Category: Isomerase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Pentose phosphate pathway]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 16:01:45 2010''