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| | <StructureSection load='6sim' size='340' side='right'caption='[[6sim]], [[Resolution|resolution]] 1.61Å' scene=''> | | <StructureSection load='6sim' size='340' side='right'caption='[[6sim]], [[Resolution|resolution]] 1.61Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6sim]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SIM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6sim]] 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=6SIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SIM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6101803Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6sim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sim OCA], [http://pdbe.org/6sim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sim RCSB], [http://www.ebi.ac.uk/pdbsum/6sim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sim ProSAT]</span></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=6sim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sim OCA], [https://pdbe.org/6sim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sim RCSB], [https://www.ebi.ac.uk/pdbsum/6sim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sim ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6sim" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6sim" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Lysozyme 3D structures|Lysozyme 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | [[Category: Gallus gallus]] | | [[Category: Gallus gallus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lysozyme]]
| + | [[Category: Garcia-Bonete MJ]] |
| - | [[Category: Garcia-Bonete, M J]] | + | [[Category: Katona G]] |
| - | [[Category: Katona, G]] | + | |
| - | [[Category: Hen egg white lysozyme]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Inverse beam geometry collection]]
| + | |
| - | [[Category: Single-wavelength x-ray anomalous diffraction]]
| + | |
| - | [[Category: Univariate analysis]]
| + | |
| Structural highlights
Function
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.[1]
Publication Abstract from PubMed
Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel's reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(-) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet's pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel's pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.
Bayesian machine learning improves single-wavelength anomalous diffraction phasing.,Garcia-Bonete MJ, Katona G Acta Crystallogr A Found Adv. 2019 Nov 1;75(Pt 6):851-860. doi:, 10.1107/S2053273319011446. Epub 2019 Oct 7. PMID:31692460[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Maehashi K, Matano M, Irisawa T, Uchino M, Kashiwagi Y, Watanabe T. Molecular characterization of goose- and chicken-type lysozymes in emu (Dromaius novaehollandiae): evidence for extremely low lysozyme levels in emu egg white. Gene. 2012 Jan 15;492(1):244-9. doi: 10.1016/j.gene.2011.10.021. Epub 2011 Oct, 25. PMID:22044478 doi:10.1016/j.gene.2011.10.021
- ↑ Garcia-Bonete MJ, Katona G. Bayesian machine learning improves single-wavelength anomalous diffraction phasing. Acta Crystallogr A Found Adv. 2019 Nov 1;75(Pt 6):851-860. doi:, 10.1107/S2053273319011446. Epub 2019 Oct 7. PMID:31692460 doi:http://dx.doi.org/10.1107/S2053273319011446
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