6qrt: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-'''Unreleased structure'''
-The entry 6qrt is ON HOLD  until Paper Publication
+==X-ray radiation dose series on xylose isomerase - 1.38 MGy==
+<StructureSection load='6qrt' size='340' side='right'caption='[[6qrt]], [[Resolution|resolution]] 1.17&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6qrt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QRT 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]] 1.17&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6qrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qrt OCA], [https://pdbe.org/6qrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qrt RCSB], [https://www.ebi.ac.uk/pdbsum/6qrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qrt ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13-3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.
-Authors:
+Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.,Taberman H, Bury CS, van der Woerd MJ, Snell EH, Garman EF J Synchrotron Radiat. 2019 Jul 1;26(Pt 4):931-944. doi:, 10.1107/S1600577519005599. Epub 2019 Jun 24. PMID:31274415<ref>PMID:31274415</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6qrt" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[D-xylose isomerase 3D structures|D-xylose isomerase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Streptomyces rubiginosus]]
+[[Category: Bury CS]]
+[[Category: Garman EF]]
+[[Category: Snell EH]]
+[[Category: Taberman H]]
+[[Category: Van der Woerd MJ]]