2vnp

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(New page: 200px<br /><applet load="2vnp" size="350" color="white" frame="true" align="right" caption="2vnp, resolution 2.19&Aring;" /> '''MONOCLINIC FORM OF IDI-1'''<br /> =...)
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[[Image:2vnp.jpg|left|200px]]<br /><applet load="2vnp" size="350" color="white" frame="true" align="right" caption="2vnp, resolution 2.19&Aring;" />
 
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'''MONOCLINIC FORM OF IDI-1'''<br />
 
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==About this Structure==
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==Monoclinic form of IDI-1==
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2VNP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=DED:'>DED</scene> as [[ligands]]. This structure supersedes the now removed PDB entry 2VEH. Active as [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] Known structural/functional Sites: <scene name='pdbsite=AC1:Binding+Site+For+Residue+Mn+A+1180'>AC1</scene>, <scene name='pdbsite=AC2:Binding+Site+For+Residue+Mg+A+1181'>AC2</scene>, <scene name='pdbsite=AC3:Binding+Site+For+Residue+Ded+A+1182'>AC3</scene>, <scene name='pdbsite=AC4:Binding+Site+For+Residue+Mn+B+1184'>AC4</scene>, <scene name='pdbsite=AC5:Binding+Site+For+Residue+Mg+B+1185'>AC5</scene> and <scene name='pdbsite=AC6:Binding+Site+For+Residue+Ded+B+1186'>AC6</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VNP OCA].
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<StructureSection load='2vnp' size='340' side='right'caption='[[2vnp]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
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[[Category: Escherichia coli]]
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== Structural highlights ==
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[[Category: Isopentenyl-diphosphate Delta-isomerase]]
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<table><tr><td colspan='2'>[[2vnp]] 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=2veh 2veh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VNP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VNP FirstGlance]. <br>
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[[Category: Single protein]]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.19&#8491;</td></tr>
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[[Category: Oudjama, Y.]]
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DED:2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE'>DED</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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[[Category: Ruyck, J De.]]
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vnp OCA], [https://pdbe.org/2vnp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vnp RCSB], [https://www.ebi.ac.uk/pdbsum/2vnp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vnp ProSAT]</span></td></tr>
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[[Category: Wouters, J.]]
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</table>
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[[Category: DED]]
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== Function ==
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[[Category: MG]]
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[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>
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[[Category: MN]]
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== Evolutionary Conservation ==
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[[Category: cytoplasm]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: ipp isomerase]]
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Check<jmol>
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[[Category: isomerase]]
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<jmolCheckbox>
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[[Category: isoprene biosynthesis]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vn/2vnp_consurf.spt"</scriptWhenChecked>
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[[Category: magnesium]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: manganese]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: metal-binding]]
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</jmolCheckbox>
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[[Category: polymorphism]]
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</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=2vnp ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 19 14:30:23 2008''
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2vnp" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia coli BL21]]
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[[Category: Large Structures]]
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[[Category: Oudjama Y]]
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[[Category: Wouters J]]
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[[Category: De Ruyck J]]

Current revision

Monoclinic form of IDI-1

PDB ID 2vnp

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