7s2f: Difference between revisions
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==Crystal structure of hen egg white lysozyme== | ==Crystal structure of hen egg white lysozyme== | ||
<StructureSection load='7s2f' size='340' side='right'caption='[[7s2f]]' scene=''> | <StructureSection load='7s2f' size='340' side='right'caption='[[7s2f]], [[Resolution|resolution]] 1.58Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S2F FirstGlance]. <br> | <table><tr><td colspan='2'>[[7s2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S2F FirstGlance]. <br> | ||
</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=7s2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s2f OCA], [https://pdbe.org/7s2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s2f RCSB], [https://www.ebi.ac.uk/pdbsum/7s2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s2f ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=7s2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s2f OCA], [https://pdbe.org/7s2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s2f RCSB], [https://www.ebi.ac.uk/pdbsum/7s2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s2f ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Reproducibility determines the utility of a measurement. In structural biology the reproducibility permeate areas such as mechanics, data measurement, data analysis and refinement. In order to access the reproducibility of the combined contribution of these sources in uncertainties of protein crystallography we evaluated four groups of parameters from data collection to final structural model. We used lysozyme as a model, with 20 datasets collected at 1.6 A resolution using two dissimilar x-ray diffraction setups and refined through a single automatic pipeline without arbitrary interpretation. Besides statistical differences in some structural parameters, the reproducibility of the final refined models allowed the determination of positional uncertainty, in good agreement with the Luzzati coordinate error. While the raw B-factor was found non-reproducible, an empirical scaling/normalization resulted in reproducible B-factors. The validity of this empirical scaling was corroborated by the reproducibility of normalized B-factors of independently solved datasets from proteins (insulin and myoglobin) from varying space groups available from structural database. The reproducibility of normalized B-factor may reposition this displacement parameter in the analysis of chemical (ligands, pH) and physical (pressure, temperature, space groups) variables. | |||
The reproducible normality of the crystallographic B-factor.,Ramos NG, Sarmanho GF, de Sa Ribeiro F, de Souza V, Lima LMTR Anal Biochem. 2022 May 15;645:114594. doi: 10.1016/j.ab.2022.114594. Epub 2022, Feb 18. PMID:35189095<ref>PMID:35189095</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7s2f" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Gallus gallus]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Lima LMTR]] | [[Category: Lima LMTR]] | ||
[[Category: Ramos NG]] | [[Category: Ramos NG]] | ||
[[Category: Ribeiro FS]] | [[Category: Ribeiro FS]] | ||