5d9b: Difference between revisions

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-'''Unreleased structure'''
-The entry 5d9b is ON HOLD
+==Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data)==
+<StructureSection load='5d9b' size='340' side='right'caption='[[5d9b]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5d9b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Photinus_pyralis Photinus pyralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D9B FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=5d9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d9b OCA], [https://pdbe.org/5d9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d9b RCSB], [https://www.ebi.ac.uk/pdbsum/5d9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d9b ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q95YI4_PHOPY Q95YI4_PHOPY]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) holds great potential for structure determination of challenging proteins that are not amenable to producing large well diffracting crystals. Efficient de novo phasing methods are highly demanding and as such most SFX structures have been determined by molecular replacement methods. Here we employed single isomorphous replacement with anomalous scattering (SIRAS) for phasing and demonstrate successful application to SFX de novo phasing. Only about 20,000 patterns in total were needed for SIRAS phasing while single wavelength anomalous dispersion (SAD) phasing was unsuccessful with more than 80,000 patterns of derivative crystals. We employed high energy X-rays from SACLA (12.6 keV) to take advantage of the large anomalous enhancement near the LIII absorption edge of Hg, which is one of the most widely used heavy atoms for phasing in conventional protein crystallography. Hard XFEL is of benefit for de novo phasing in the use of routinely used heavy atoms and high resolution data collection.
-Authors: Yamashita, K., Pan, D., Okuda, T., Murai, T., Kodan, A., Yamaguchi, T., Gomi, K., Kajiyama, N., Kato, H., Ago, H., Yamamoto, M., Nakatsu, T.
+An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.,Yamashita K, Pan D, Okuda T, Sugahara M, Kodan A, Yamaguchi T, Murai T, Gomi K, Kajiyama N, Mizohata E, Suzuki M, Nango E, Tono K, Joti Y, Kameshima T, Park J, Song C, Hatsui T, Yabashi M, Iwata S, Kato H, Ago H, Yamamoto M, Nakatsu T Sci Rep. 2015 Sep 11;5:14017. doi: 10.1038/srep14017. PMID:26360462<ref>PMID:26360462</ref>
-Description: Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Murai, T]]
+<div class="pdbe-citations 5d9b" style="background-color:#fffaf0;"></div>
-[[Category: Yamamoto, M]]
+== References ==
-[[Category: Kato, H]]
+<references/>
-[[Category: Okuda, T]]
+__TOC__
-[[Category: Pan, D]]
+</StructureSection>
-[[Category: Yamashita, K]]
+[[Category: Large Structures]]
-[[Category: Gomi, K]]
+[[Category: Photinus pyralis]]
-[[Category: Kodan, A]]
+[[Category: Ago H]]
-[[Category: Ago, H]]
+[[Category: Gomi K]]
-[[Category: Nakatsu, T]]
+[[Category: Kajiyama N]]
-[[Category: Kajiyama, N]]
+[[Category: Kato H]]
-[[Category: Yamaguchi, T]]
+[[Category: Kodan A]]
+[[Category: Murai T]]
+[[Category: Nakatsu T]]
+[[Category: Okuda T]]
+[[Category: Pan D]]
+[[Category: Yamaguchi T]]
+[[Category: Yamamoto M]]
+[[Category: Yamashita K]]