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4emq

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==Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4==
==Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4==
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<StructureSection load='4emq' size='340' side='right' caption='[[4emq]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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<StructureSection load='4emq' size='340' side='right'caption='[[4emq]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4emq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Echinophyllia_sp._sc22 Echinophyllia sp. sc22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EMQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EMQ FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4emq]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Echinophyllia_sp._SC22 Echinophyllia sp. SC22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EMQ FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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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]] 1.95&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GYC:[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>GYC</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2z1o|2z1o]], [[2z6y|2z6y]], [[2z6z|2z6z]]</td></tr>
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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=4emq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4emq OCA], [https://pdbe.org/4emq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4emq RCSB], [https://www.ebi.ac.uk/pdbsum/4emq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4emq ProSAT]</span></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dronpa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301887 Echinophyllia sp. SC22])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4emq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4emq OCA], [http://pdbe.org/4emq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4emq RCSB], [http://www.ebi.ac.uk/pdbsum/4emq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4emq ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q5TLG6_9CNID Q5TLG6_9CNID]
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The crystal structure of the on-state of PDM1-4, a single-mutation variant of the photochromic fluorescent protein Dronpa, is reported at 1.95 A resolution. PDM1-4 is a Dronpa variant that possesses a slower off-switching rate than Dronpa and thus can effectively increase the image resolution in subdiffraction optical microscopy, although the precise molecular basis for this change has not been elucidated. This work shows that the Lys145Asn mutation in PDM1-4 stabilizes the interface available for dimerization, facilitating oligomerization of the protein. No significant changes were observed in the chromophore environment of PDM1-4 compared with Dronpa, and the ensemble absorption and emission properties of PDM1-4 were highly similar to those of Dronpa. It is proposed that the slower off-switching rate in PDM1-4 is caused by a decrease in the potential flexibility of certain beta-strands caused by oligomerization along the AC interface.
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Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa.,Nguyen Bich N, Moeyaert B, Van Hecke K, Dedecker P, Mizuno H, Hofkens J, Van Meervelt L Acta Crystallogr D Biol Crystallogr. 2012 Dec;68(Pt 12):1653-9. doi:, 10.1107/S0907444912039686. Epub 2012 Nov 9. PMID:23151630<ref>PMID:23151630</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 4emq" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Dronpa|Dronpa]]
*[[Dronpa|Dronpa]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Echinophyllia sp. sc22]]
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[[Category: Echinophyllia sp. SC22]]
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[[Category: Hecke, K Van]]
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[[Category: Large Structures]]
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[[Category: Meervelt, L Van]]
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[[Category: Ngan NB]]
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[[Category: Ngan, N B]]
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[[Category: Van Hecke K]]
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[[Category: Beta barrel]]
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[[Category: Van Meervelt L]]
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[[Category: Dronpa]]
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[[Category: Fluorescent protein]]
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[[Category: Gfp-like protein]]
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[[Category: Reversible photoswitchable fluorescent protein]]
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Current revision

Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4

PDB ID 4emq

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