6syd - Revision history

OCA at 12:50, 24 January 2024

OCA — Wed, 24 Jan 2024 12:50:19 GMT

←Older revision		Revision as of 12:50, 24 January 2024
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	<StructureSection load='6syd' size='340' side='right'caption='[[6syd]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='6syd' size='340' side='right'caption='[[6syd]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6syd]] 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=6SYD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6SYD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6syd]] 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=6SYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SYD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=LYE:bromophenol+blue'>LYE</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]] 1.1Å</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=LYE:bromophenol+blue'>LYE</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~~://proteopedia.org/fgij/fg.htm?mol=6syd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6syd OCA], [~~http~~://pdbe.org/6syd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6syd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6syd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6syd 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=6syd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6syd OCA], [https://pdbe.org/6syd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6syd RCSB], [https://www.ebi.ac.uk/pdbsum/6syd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6syd 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 6syd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6syd" 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: Camara-Artigas A]]
-	[[Category: Camara-Artigas, A]]	+	[[Category: Plaza-Garrido M]]
-	[[Category: Plaza-Garrido, M]]	+	[[Category: Salinas-Garcia MC]]
-	[[Category: Salinas-Garcia~~, M C]]~~	+
-	~~[[Category: Dye-soaking]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:09, 16 September 2020

OCA — Wed, 16 Sep 2020 10:09:40 GMT

←Older revision		Revision as of 10:09, 16 September 2020
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	==Crystal structure of the lysozyme in presence of bromophenol blue at pH 5.5==		==Crystal structure of the lysozyme in presence of bromophenol blue at pH 5.5==
-	<StructureSection load='6syd' size='340' side='right'caption='[[6syd]]' scene=''>	+	<StructureSection load='6syd' size='340' side='right'caption='[[6syd]], [[Resolution\|resolution]] 1.10Å' 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=6SYD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SYD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6syd]] 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=6SYD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SYD FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6syd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6syd OCA], [http://pdbe.org/6syd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6syd RCSB], [http://www.ebi.ac.uk/pdbsum/6syd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6syd 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=LYE:bromophenol+blue'>LYE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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'>[http://proteopedia.org/fgij/fg.htm?mol=6syd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6syd OCA], [http://pdbe.org/6syd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6syd RCSB], [http://www.ebi.ac.uk/pdbsum/6syd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6syd ProSAT]</span></td></tr>
	</table>		</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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein-dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme-bromophenol blue crystals: binding site I is located near the amino- and carboxyl-termini, while binding site II is located adjacent to helices alpha1 (residues 4-15) and alpha3 (residues 88-100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL-T1) show a single dye molecule bound to site II, and the crystals belong to space group P43212 without significant changes in the unit cell (a = b = 78.50, c = 37.34 A). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL-T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P212121) and unit cell (a = 38.00, b = 76.65, c = 84.86 A). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions.
		+
		+	Lysozyme crystals dyed with bromophenol blue: where has the dye gone?,Plaza-Garrido M, Salinas-Garcia MC, Alba-Elena D, Martinez JC, Camara-Artigas A Acta Crystallogr D Struct Biol. 2020 Sep 1;76(Pt 9):845-856. doi:, 10.1107/S2059798320008803. Epub 2020 Sep 1. PMID:32876060<ref>PMID:32876060</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6syd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Camara-Artigas A]]	+	[[Category: Lysozyme]]
-	[[Category: Plaza-Garrido M]]	+	[[Category: Camara-Artigas, A]]
-	[[Category: Salinas-Garcia MC]]	+	[[Category: Plaza-Garrido, M]]
		+	[[Category: Salinas-Garcia, M C]]
		+	[[Category: Dye-soaking]]
		+	[[Category: Glycosidase]]
		+	[[Category: Hydrolase]]

OCA at 09:31, 9 September 2020

OCA — Wed, 09 Sep 2020 09:31:43 GMT

←Older revision		Revision as of 09:31, 9 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6syd ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the lysozyme in presence of bromophenol blue at pH 5.5==
-		+	<StructureSection load='6syd' size='340' side='right'caption='[[6syd]]' scene=''>
-	~~Authors~~: ~~Camara~~-~~Artigas, A~~., ~~Plaza~~-~~Garrido~~, M., ~~Salinas-Garcia~~, M.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SYD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SYD FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of the lysozyme in presence of bromophenol blue at pH 5~~.5	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6syd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6syd OCA], [http://pdbe.org/6syd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6syd RCSB], [http://www.ebi.ac.uk/pdbsum/6syd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6syd ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Salinas~~-~~Garcia, M.C~~]]	+	__TOC__
-	[[Category: Plaza-Garrido, M]]	+	</StructureSection>
-	[[Category: ~~Camara~~-~~Artigas, A~~]]	+	[[Category: Large Structures]]
		+	[[Category: Camara-Artigas A]]
		+	[[Category: Plaza-Garrido M]]
		+	[[Category: Salinas-Garcia MC]]

OCA at 10:35, 8 July 2020

OCA — Wed, 08 Jul 2020 10:35:48 GMT

←Older revision		Revision as of 10:35, 8 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6syd is ON HOLD	+	The entry 6syd is ON HOLD until Paper Publication

	Authors: Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.		Authors: Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.

OCA at 04:36, 27 May 2020

OCA — Wed, 27 May 2020 04:36:43 GMT

←Older revision		Revision as of 04:36, 27 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6syd is ON HOLD ~~until Paper Publication~~	+	The entry 6syd is ON HOLD

	Authors: Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.		Authors: Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.

OCA: Protected "6syd" [edit=sysop:move=sysop]

OCA — Thu, 10 Oct 2019 03:42:41 GMT

Protected "6syd" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:42, 10 October 2019

OCA: New page: '''Unreleased structure''' The entry 6syd is ON HOLD until Paper Publication Authors: Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C. Description: Crystal structure of the ...

OCA — Thu, 10 Oct 2019 03:42:39 GMT

New page: '''Unreleased structure''' The entry 6syd is ON HOLD until Paper Publication Authors: Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C. Description: Crystal structure of the ...

New page

'''Unreleased structure'''

The entry 6syd is ON HOLD until Paper Publication

Authors: Camara-Artigas, A., Plaza-Garrido, M., Salinas-Garcia, M.C.

Description: Crystal structure of the lysozyme in presence of bromophenol blue at pH 5.5
[[Category: Unreleased Structures]]
[[Category: Salinas-Garcia, M.C]]
[[Category: Plaza-Garrido, M]]
[[Category: Camara-Artigas, A]]