This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2vnp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:26, 13 December 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2vnp.jpg|left|200px]]
 
-
<!--
+
==Monoclinic form of IDI-1==
-
The line below this paragraph, containing "STRUCTURE_2vnp", creates the "Structure Box" on the page.
+
<StructureSection load='2vnp' size='340' side='right'caption='[[2vnp]], [[Resolution|resolution]] 2.19&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'>[[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>
-
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]] 2.19&#8491;</td></tr>
-
-->
+
<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>
-
{{STRUCTURE_2vnp| PDB=2vnp | SCENE= }}
+
<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>
 +
</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/2vnp_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=2vnp 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 2vnp" style="background-color:#fffaf0;"></div>
-
==About this Structure==
+
==See Also==
-
2VNP 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 [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].
+
*[[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: Cytoplasm]]
+
[[Category: Oudjama Y]]
-
[[Category: Ipp isomerase]]
+
[[Category: Wouters J]]
-
[[Category: Isomerase]]
+
[[Category: De Ruyck J]]
-
[[Category: Isoprene biosynthesis]]
+
-
[[Category: Magnesium]]
+
-
[[Category: Manganese]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Polymorphism]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 19:03:04 2008''
+

Current revision

Monoclinic form of IDI-1

PDB ID 2vnp

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vnp"
Personal tools