2vnq: Difference between revisions

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-[[Image:2vnq.jpg|left|200px]]
- {{Structure
+==Monoclinic form of IDI-1==
-|PDB= 2vnq |SIZE=350|CAPTION= <scene name='initialview01'>2vnq</scene>, resolution 2.20&Aring;
+<StructureSection load='2vnq' size='340' side='right'caption='[[2vnq]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Binding+Site+For+Residue+Mn+A+201'>AC1</scene>, <scene name='pdbsite=AC2:Binding+Site+For+Residue+Imd+A+301'>AC2</scene>, <scene name='pdbsite=AC3:Binding+Site+For+Residue+So4+A+401'>AC3</scene>, <scene name='pdbsite=AC4:Binding+Site+For+Residue+Mn+B+201'>AC4</scene>, <scene name='pdbsite=AC5:Binding+Site+For+Residue+Imd+B+301'>AC5</scene> and <scene name='pdbsite=AC6:Binding+Site+For+Residue+So4+B+401'>AC6</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>
+<table><tr><td colspan='2'>[[2vnq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21 Escherichia coli BL21]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vej 2vej]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VNQ FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Isopentenyl-diphosphate_Delta-isomerase Isopentenyl-diphosphate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.2 5.3.3.2]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <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=2vnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vnq OCA], [https://pdbe.org/2vnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vnq RCSB], [https://www.ebi.ac.uk/pdbsum/2vnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vnq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IDI_ECOLI IDI_ECOLI] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).<ref>PMID:10099534</ref> <ref>PMID:9603997</ref>
+== 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/vn/2vnq_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=2vnq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Type 1 isopentenyl diphosphate isomerase (IDI-1) has been crystallized in a new crystal form. After data collection from small thin needle-shaped crystals, a new monoclinic form of the studied protein was identified. In this article, the three crystal forms of IDI-1 (orthorhombic, monoclinic and trigonal) are compared.
-'''MONOCLINIC FORM OF IDI-1'''
+Monoclinic form of isopentenyl diphosphate isomerase: a case of polymorphism in biomolecular crystals.,de Ruyck J, Oudjama Y, Wouters J Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Apr 1;64(Pt, 4):239-42. Epub 2008 Mar 21. PMID:18391416<ref>PMID:18391416</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vnq" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-VNQ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry 2VEJ. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VNQ OCA].
+*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
-[[Category: Escherichia coli]]
+== References ==
-[[Category: Isopentenyl-diphosphate Delta-isomerase]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Oudjama, Y.]]
+</StructureSection>
-[[Category: Ruyck, J De.]]
+[[Category: Escherichia coli BL21]]
-[[Category: Wouters, J.]]
+[[Category: Large Structures]]
-[[Category: IMD]]
+[[Category: Oudjama Y]]
-[[Category: MN]]
+[[Category: Wouters J]]
-[[Category: SO4]]
+[[Category: De Ruyck J]]
-[[Category: cytoplasm]]
-[[Category: ipp isomerase]]
-[[Category: isomerase]]
-[[Category: isoprene biosynthesis]]
-[[Category: magnesium]]
-[[Category: manganese]]
-[[Category: metal-binding]]
-[[Category: polymorphism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 09:31:35 2008''