8sog: 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 8sog is ON HOLD
+==Proteinase K Multiconformer Model at 313K==
+<StructureSection load='8sog' size='340' side='right'caption='[[8sog]], [[Resolution|resolution]] 1.13&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8sog]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Parengyodontium_album Parengyodontium album]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8SOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8SOG 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]] 1.13&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8sog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8sog OCA], [https://pdbe.org/8sog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8sog RCSB], [https://www.ebi.ac.uk/pdbsum/8sog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8sog ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRTK_PARAQ PRTK_PARAQ] Hydrolyzes keratin at aromatic and hydrophobic residues.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Conformational ensembles underlie all protein functions. Thus, acquiring atomic-level ensemble models that accurately represent conformational heterogeneity is vital to deepen our understanding of how proteins work. Modeling ensemble information from X-ray diffraction data has been challenging, as traditional cryo-crystallography restricts conformational variability while minimizing radiation damage. Recent advances have enabled the collection of high quality diffraction data at ambient temperatures, revealing innate conformational heterogeneity and temperature-driven changes. Here, we used diffraction datasets for Proteinase K collected at temperatures ranging from 313 to 363 K to provide a tutorial for the refinement of multiconformer ensemble models. Integrating automated sampling and refinement tools with manual adjustments, we obtained multiconformer models that describe alternative backbone and sidechain conformations, their relative occupancies, and interconnections between conformers. Our models revealed extensive and diverse conformational changes across temperature, including increased bound peptide ligand occupancies, different Ca(2+) binding site configurations and altered rotameric distributions. These insights emphasize the value and need for multiconformer model refinement to extract ensemble information from diffraction data and to understand ensemble-function relationships.
-Authors:
+Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.,Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS Methods Enzymol. 2023;688:223-254. doi: 10.1016/bs.mie.2023.06.009. Epub 2023 Jul , 27. PMID:37748828<ref>PMID:37748828</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 8sog" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Proteinase 3D structures|Proteinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Parengyodontium album]]
+[[Category: Doukov T]]
+[[Category: Du S]]
+[[Category: Fraser JS]]
+[[Category: Herschlag D]]
+[[Category: Wankowicz S]]
+[[Category: Yabukarski F]]