6rt9 - Revision history

OCA at 12:27, 24 January 2024

2024-01-24T12:27:56Z

←Older revision		Revision as of 12:27, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6rt9' size='340' side='right'caption='[[6rt9]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6rt9' size='340' side='right'caption='[[6rt9]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rt9]] 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=6RT9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6RT9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rt9]] 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=6RT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RT9 FirstGlance]. <br>
-	</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>, <scene name='pdbligand=GLC:ALPHA~~-~~D-GLUCOSE'>GLC</scene>~~, ~~<scene name='pdbligand=FRU:FRUCTOSE'>FRU</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]] 1.55Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6rt1\|6rt1]], [[6rt3\|6rt3]]~~<~~/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>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</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=6rt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rt9 OCA], [https://pdbe.org/6rt9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rt9 RCSB], [https://www.ebi.ac.uk/pdbsum/6rt9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rt9 ProSAT]</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=6rt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rt9 OCA], [~~http~~://pdbe.org/6rt9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rt9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rt9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rt9 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 ==
Line 29:		Line 28:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Ferreira C]]
-	[[Category: Ferreira, C]]	+	[[Category: Martins PM]]
-	[[Category: Martins~~, P M~~]]	+	[[Category: Pereira PJB]]
-	[[Category: Pereira~~, P J.B]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 05:50, 5 August 2020

2020-08-05T05:50:20Z

←Older revision		Revision as of 05:50, 5 August 2020
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6rt9]] 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=6RT9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RT9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6rt9]] 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=6RT9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RT9 FirstGlance]. <br>
-	</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>, <scene name='pdbligand=~~SUC~~:~~SUCROSE~~'>~~SUC~~</scene></td></tr>	+	</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>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rt1\|6rt1]], [[6rt3\|6rt3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rt1\|6rt1]], [[6rt3\|6rt3]]</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='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>

OCA at 11:26, 22 July 2020

2020-07-22T11:26:04Z

←Older revision		Revision as of 11:26, 22 July 2020
Line 3:		Line 3:
	<StructureSection load='6rt9' size='340' side='right'caption='[[6rt9]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6rt9' size='340' side='right'caption='[[6rt9]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rt9]] 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=6RT9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RT9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rt9]] 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=6RT9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RT9 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>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>	+	</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>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rt1\|6rt1]], [[6rt3\|6rt3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rt1\|6rt1]], [[6rt3\|6rt3]]</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='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://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6rt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rt9 OCA], [http://pdbe.org/6rt9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rt9 RCSB], [http://www.ebi.ac.uk/pdbsum/6rt9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rt9 ProSAT]</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=6rt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rt9 OCA], [http://pdbe.org/6rt9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rt9 RCSB], [http://www.ebi.ac.uk/pdbsum/6rt9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rt9 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>		[[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 ==
		+	When placed in the same environment, biochemically unrelated macromolecules influence each other's biological function through macromolecular crowding (MC) effects. This has been illustrated in vitro by the effects of inert polymers on protein stability, protein structure, enzyme kinetics and protein aggregation kinetics. While a unified way to quantitatively characterize MC is still lacking, we show that the crystal solubility of lysozyme can be used to predict the influence of crowding agents on the catalytic efficiency of this enzyme. In order to capture general enthalpic effects, as well as hard entropic effects that are specific of large molecules, we tested sucrose and its cross-linked polymer Ficoll-70 as additives. Despite the different conditions of pH and ionic strength adopted, both the crystallization and the enzymatic assays point to an entropic contribution of approximately -1 kcal mol-1 caused by MC. Our results demonstrate that the thermodynamic activity of proteins is markedly increased by the reduction of accessible volume caused by the presence of macromolecular cosolutes. Unlike what is observed in protein folding studies, this MC effect cannot be reproduced using equivalent concentrations of monomeric crowding units. Applicable to any crystallizable protein, the thermodynamic interpretation of MC based on crystal solubility is expected to help in elucidating the full extent and importance of hard-type interactions in the crowded environment of the cell.
		+
		+	Protein crystals as a key for deciphering macromolecular crowding effects on biological reactions.,Ferreira C, Pinto MF, Macedo-Ribeiro S, Pereira PJB, Rocha FA, Martins PM Phys Chem Chem Phys. 2020 Jul 8. doi: 10.1039/d0cp02469d. PMID:32638771<ref>PMID:32638771</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6rt9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:55, 5 June 2019

2019-06-05T22:55:55Z

←Older revision		Revision as of 22:55, 5 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6rt9 is ~~ON HOLD~~	+	==Orthorhombic lysozyme grown with 300g/L sucrose==
-		+	<StructureSection load='6rt9' size='340' side='right'caption='[[6rt9]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~Authors~~: ~~Pereira~~, P.J.B., ~~Ferreira~~, C., ~~Martins~~, P.M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6rt9]] 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=6RT9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RT9 FirstGlance]. <br>
-	~~Description~~: ~~Orthorhombic lysozyme grown~~ with ~~300g~~/~~L sucrose~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rt1\|6rt1]], [[6rt3\|6rt3]]</td></tr>
-	[[Category: ~~Martins, P.M~~]]	+	<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>
-	[[Category: ~~Pereira, P.J.B~~]]	+	<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=6rt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rt9 OCA], [http://pdbe.org/6rt9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rt9 RCSB], [http://www.ebi.ac.uk/pdbsum/6rt9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rt9 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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gallus gallus]]
		+	[[Category: Large Structures]]
		+	[[Category: Lysozyme]]
	[[Category: Ferreira, C]]		[[Category: Ferreira, C]]
		+	[[Category: Martins, P M]]
		+	[[Category: Pereira, P J.B]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA: Protected "6rt9" [edit=sysop:move=sysop]

2019-05-29T04:48:38Z

Protected "6rt9" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:48, 29 May 2019

OCA: New page: '''Unreleased structure''' The entry 6rt9 is ON HOLD Authors: Pereira, P.J.B., Ferreira, C., Martins, P.M. Description: Orthorhombic lysozyme grown with 300g/L sucrose [[Category: Unre...

2019-05-29T04:48:37Z

New page: '''Unreleased structure''' The entry 6rt9 is ON HOLD Authors: Pereira, P.J.B., Ferreira, C., Martins, P.M. Description: Orthorhombic lysozyme grown with 300g/L sucrose [[Category: Unre...

New page

'''Unreleased structure'''

The entry 6rt9 is ON HOLD

Authors: Pereira, P.J.B., Ferreira, C., Martins, P.M.

Description: Orthorhombic lysozyme grown with 300g/L sucrose
[[Category: Unreleased Structures]]
[[Category: Martins, P.M]]
[[Category: Pereira, P.J.B]]
[[Category: Ferreira, C]]