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2xbr

From Proteopedia

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Raman crystallography of Hen White Egg Lysozyme - Low X-ray dose (0.2 MGy)

Structural highlights

2xbr is a 1 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.29Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

X-ray-induced chemistry modifies biological macromolecules structurally and functionally, even at cryotemperatures. The mechanisms of x-radiation damage in colored or redox proteins have often been investigated by combining X-ray crystallography with in crystallo ultraviolet-visible spectroscopy. Here, we used Raman microspectrophotometry to follow the onset of damage in crystalline lysozyme, notably that of disulfide bond breakage. The dose-dependent Raman spectra are consistent with a kinetic model for the rupture of disulfide bonds suggesting the rapid build up of an anionic radical intermediate. This intermediate may either revert back to the oxidized state or evolve toward protonated radical species or cleaved products. The data strongly suggest that back conversion of the anionic radical is significantly accelerated by X-rays, revealing an X-ray-induced "repair" mechanism. The possibility of X-ray-induced chemical repair is an important feature to take into account when assessing radiation damage in macromolecules.

Raman-assisted crystallography suggests a mechanism of x-ray-induced disulfide radical formation and reparation.,Carpentier P, Royant A, Weik M, Bourgeois D Structure. 2010 Nov 10;18(11):1410-9. PMID:21070940^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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
↑ Carpentier P, Royant A, Weik M, Bourgeois D. Raman-assisted crystallography suggests a mechanism of x-ray-induced disulfide radical formation and reparation. Structure. 2010 Nov 10;18(11):1410-9. PMID:21070940 doi:10.1016/j.str.2010.09.010

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xbr"

@@ Line 1: / Line 1: @@
 ==Raman crystallography of Hen White Egg Lysozyme - Low X-ray dose (0.2 MGy)==
-<StructureSection load='2xbr' size='340' side='right' caption='[[2xbr]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
+<StructureSection load='2xbr' size='340' side='right'caption='[[2xbr]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xbr]] 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=2XBR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XBR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xbr]] 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=2XBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XBR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.29&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1w6z|1w6z]], [[1kxx|1kxx]], [[3lyo|3lyo]], [[4lyo|4lyo]], [[1t6v|1t6v]], [[1kip|1kip]], [[1ic7|1ic7]], [[1vds|1vds]], [[1lzt|1lzt]], [[1kir|1kir]], [[1lys|1lys]], [[1e8l|1e8l]], [[1bwj|1bwj]], [[132l|132l]], [[1yil|1yil]], [[1heo|1heo]], [[1sfg|1sfg]], [[1kxw|1kxw]], [[2x0a|2x0a]], [[2c8o|2c8o]], [[1g7l|1g7l]], [[1yl1|1yl1]], [[1sf4|1sf4]], [[1ior|1ior]], [[1h87|1h87]], [[1ljg|1ljg]], [[3lyt|3lyt]], [[1dpx|1dpx]], [[1iot|1iot]], [[1v7s|1v7s]], [[1ja6|1ja6]], [[1jis|1jis]], [[1ir8|1ir8]], [[2w1m|2w1m]], [[1uic|1uic]], [[1xgq|1xgq]], [[1ykz|1ykz]], [[1uie|1uie]], [[2war|2war]], [[1lji|1lji]], [[1lj3|1lj3]], [[1dpw|1dpw]], [[8lyz|8lyz]], [[1bwi|1bwi]], [[2iff|2iff]], [[2lyo|2lyo]], [[1g7h|1g7h]], [[1lks|1lks]], [[1jj0|1jj0]], [[1rfp|1rfp]], [[5lyt|5lyt]], [[1sfb|1sfb]], [[1jiy|1jiy]], [[1ir7|1ir7]], [[1iee|1iee]], [[1xei|1xei]], [[1xek|1xek]], [[1hel|1hel]], [[1at6|1at6]], [[1ljf|1ljf]], [[1mlc|1mlc]], [[2b5z|2b5z]], [[1f10|1f10]], [[1lsz|1lsz]], [[193l|193l]], [[1ljk|1ljk]], [[6lyt|6lyt]], [[1sq2|1sq2]], [[1zmy|1zmy]], [[1vdq|1vdq]], [[1lje|1lje]], [[2d91|2d91]], [[1lze|1lze]], [[1b2k|1b2k]], [[1aki|1aki]], [[1uia|1uia]], [[1hen|1hen]], [[1xfp|1xfp]], [[1yik|1yik]], [[2d6b|2d6b]], [[1ndg|1ndg]], [[1lpi|1lpi]], [[1lsd|1lsd]], [[1flw|1flw]], [[2blx|2blx]], [[6lyz|6lyz]], [[1nbz|1nbz]], [[1lsg|1lsg]], [[4lyt|4lyt]], [[3hfm|3hfm]], [[1ved|1ved]], [[1jit|1jit]], [[1lzn|1lzn]], [[1uuz|1uuz]], [[1ja2|1ja2]], [[1wtn|1wtn]], [[1lyz|1lyz]], [[2d4i|2d4i]], [[2fbb|2fbb]], [[2lym|2lym]], [[1fdl|1fdl]], [[1lse|1lse]], [[1lzh|1lzh]], [[1lz9|1lz9]], [[1gxx|1gxx]], [[1lsm|1lsm]], [[1jj3|1jj3]], [[7lyz|7lyz]], [[3lym|3lym]], [[1yky|1yky]], [[1kiq|1kiq]], [[1t3p|1t3p]], [[1heq|1heq]], [[2lzh|2lzh]], [[1kxy|1kxy]], [[1uih|1uih]], [[2w1l|2w1l]], [[2bly|2bly]], [[1g7j|1g7j]], [[1b0d|1b0d]], [[1bhz|1bhz]], [[1her|1her]], [[1wtm|1wtm]], [[1hep|1hep]], [[1ioq|1ioq]], [[1nby|1nby]], [[1jtt|1jtt]], [[1qio|1qio]], [[1lza|1lza]], [[1ps5|1ps5]], [[1xgp|1xgp]], [[1gwd|1gwd]], [[1v7t|1v7t]], [[1jpo|1jpo]], [[1h6m|1h6m]], [[1j1p|1j1p]], [[2a7d|2a7d]], [[1dqj|1dqj]], [[1z55|1z55]], [[1ljj|1ljj]], [[2c8p|2c8p]], [[1lsb|1lsb]], [[1f0w|1f0w]], [[2w1x|2w1x]], [[1lzg|1lzg]], [[1flq|1flq]], [[1lzc|1lzc]], [[1jj1|1jj1]], [[1rcm|1rcm]], [[1yqv|1yqv]], [[1uid|1uid]], [[1bgi|1bgi]], [[1hsx|1hsx]], [[1lzd|1lzd]], [[1lcn|1lcn]], [[1hew|1hew]], [[2vb1|2vb1]], [[2cds|2cds]], [[2aub|2aub]], [[1uib|1uib]], [[1hf4|1hf4]], [[1rjc|1rjc]], [[1ir9|1ir9]], [[1ios|1ios]], [[1j1x|1j1x]], [[2cgi|2cgi]], [[1uc0|1uc0]], [[1azf|1azf]], [[1ic4|1ic4]], [[1ljh|1ljh]], [[4lyz|4lyz]], [[1gpq|1gpq]], [[2a6u|2a6u]], [[2d4k|2d4k]], [[1xej|1xej]], [[1ja7|1ja7]], [[1mel|1mel]], [[1ri8|1ri8]], [[1uig|1uig]], [[1bvx|1bvx]], [[1c10|1c10]], [[1qtk|1qtk]], [[1lkr|1lkr]], [[1lyo|1lyo]], [[1n4f|1n4f]], [[1hsw|1hsw]], [[1g7m|1g7m]], [[2w1y|2w1y]], [[1jto|1jto]], [[1sf7|1sf7]], [[1lsf|1lsf]], [[1fn5|1fn5]], [[5lyz|5lyz]], [[2d4j|2d4j]], [[1c08|1c08]], [[3lzt|3lzt]], [[1ndm|1ndm]], [[1sf6|1sf6]], [[3lyz|3lyz]], [[1bvk|1bvk]], [[1uif|1uif]], [[1vau|1vau]], [[2lyz|2lyz]], [[1lma|1lma]], [[1fly|1fly]], [[1hc0|1hc0]], [[1yl0|1yl0]], [[1j1o|1j1o]], [[2lzt|2lzt]], [[1a2y|1a2y]], [[4lzt|4lzt]], [[1lsy|1lsy]], [[1uco|1uco]], [[5lym|5lym]], [[1p2c|1p2c]], [[1lsa|1lsa]], [[1gxv|1gxv]], [[1ic5|1ic5]], [[1ua6|1ua6]], [[1at5|1at5]], [[1vfb|1vfb]], [[1hem|1hem]], [[1f3j|1f3j]], [[1lj4|1lj4]], [[1vat|1vat]], [[1ja4|1ja4]], [[4lym|4lym]], [[2a7f|2a7f]], [[194l|194l]], [[1flu|1flu]], [[1lz8|1lz8]], [[1ykx|1ykx]], [[1vdt|1vdt]], [[2hfm|2hfm]], [[1bwh|1bwh]], [[1io5|1io5]], [[1lsn|1lsn]], [[1g7i|1g7i]], [[2bpu|2bpu]], [[1lzb|1lzb]], [[1lsc|1lsc]], [[1vdp|1vdp]], [[2xbs|2xbs]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xbr OCA], [https://pdbe.org/2xbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xbr RCSB], [https://www.ebi.ac.uk/pdbsum/2xbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xbr ProSAT]</span></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=2xbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xbr OCA], [http://pdbe.org/2xbr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xbr RCSB], [http://www.ebi.ac.uk/pdbsum/2xbr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xbr ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 27: @@
 </StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Bourgeois, D]]
+[[Category: Bourgeois D]]
-[[Category: Carpentier, P]]
+[[Category: Carpentier P]]
-[[Category: Royant, A]]
+[[Category: Royant A]]
-[[Category: Weik, M]]
+[[Category: Weik M]]
-[[Category: Disulfide radical]]
-[[Category: Hydrolase]]
-[[Category: Radiation damage]]
-[[Category: Raman spectroscopy]]

2xbr

From Proteopedia

Current revision

Raman crystallography of Hen White Egg Lysozyme - Low X-ray dose (0.2 MGy)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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