6a4o - Revision history

OCA at 09:18, 22 November 2023

2023-11-22T09:18:19Z

←Older revision		Revision as of 09:18, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6a4o' size='340' side='right'caption='[[6a4o]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6a4o' size='340' side='right'caption='[[6a4o]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a4o]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5h6c 5h6c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6A4O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a4o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5h6c 5h6c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A4O 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=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.75Å</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6a4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4o OCA], [~~http~~://pdbe.org/6a4o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6a4o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6a4o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4o 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=6a4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4o OCA], [https://pdbe.org/6a4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a4o RCSB], [https://www.ebi.ac.uk/pdbsum/6a4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4o 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 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6a4o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6a4o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Lysozyme]]~~	+	[[Category: Hosur MV]]
-	[[Category: Hosur~~, M V~~]]	+	[[Category: Kini RM]]
-	[[Category: Kini~~, R M~~]]	+	[[Category: Koh CY]]
-	[[Category: Koh~~, C Y~~]]	+	[[Category: Tushar R]]
-	[[Category: Tushar, R]]	+
-	~~[[Category: Chemical denaturant]]~~	+
-	~~[[Category: Guanidine]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein unfolding~~]]	+

OCA at 11:47, 13 March 2019

2019-03-13T11:47:27Z

←Older revision		Revision as of 11:47, 13 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6a4o is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==HEWL crystals soaked in 2.5M GuHCl for 20 minutes==
		+	<StructureSection load='6a4o' size='340' side='right'caption='[[6a4o]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6a4o]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5h6c 5h6c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A4O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A4O 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=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6a4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a4o OCA], [http://pdbe.org/6a4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a4o RCSB], [http://www.ebi.ac.uk/pdbsum/6a4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a4o 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Time-dependent binding of guanidine hydrochloride (GuHCl) to hen egg-white lysozyme (HEWL), and effects of this binding on the protein structure have been investigated by solving X-ray structures of crystalline complexes. The complexes have been prepared by soaking, for different periods of time, native lysozyme crystals in solutions containing 2.5M GuHCl. In the refined structures, the number of water molecules in the protein's first solvent shell has progressively decreased from 152 to 115, showing protein's preference for guanidinium over water. Guanidinium ions preferentially hydrogen bond with the backbone carbonyl oxygen atoms. In their van der Waals interactions, they do not show any preference for apolar residues. Guanidinium ions have replaced water molecules that form cages around exposed hydrophobic residues. Guanidinium binding has decreased the average length of water-water hydrogen bond by 0.1A. The hydrogen bonds between main chain atoms have been weakened by GuHCl, and this may be the reason for increased potency of GuHCl compared to urea. Guanidinium binding destabilizes the beta-domain by causing loss of hydrogen bonds involving Asn 59 side chain. Interestingly, this loss is almost identical to that observed in structures of amyloidogenic variants of human lysozyme. Compounds preventing this loss could be anti-amyloidogenic.

-	~~Authors~~: ~~Tushar, R~~., Kini, R.M.~~, Koh, C~~.Y.~~, Hosur, M~~.V.	+	X-ray crystallographic analysis of time-dependent binding of guanidine hydrochloride to HEWL: First steps during protein unfolding.,Raskar T, Koh CY, Niebling S, Kini RM, Hosur MV Int J Biol Macromol. 2019 Feb 1;122:903-913. doi: 10.1016/j.ijbiomac.2018.11.023., Epub 2018 Nov 6. PMID:30412756<ref>PMID:30412756</ref>

-	~~Description: HEWL crystals soaked in 2~~.~~5M GuHCl for 20 minutes~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6a4o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gallus gallus]]
		+	[[Category: Large Structures]]
		+	[[Category: Lysozyme]]
		+	[[Category: Hosur, M V]]
		+	[[Category: Kini, R M]]
		+	[[Category: Koh, C Y]]
	[[Category: Tushar, R]]		[[Category: Tushar, R]]
-	[[Category: ~~Hosur, M.V~~]]	+	[[Category: Chemical denaturant]]
-	[[Category: ~~Koh, C.Y~~]]	+	[[Category: Guanidine]]
-	[[Category: ~~Kini, R.M~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Protein unfolding]]

OCA at 05:18, 6 March 2019

2019-03-06T05:18:45Z

←Older revision		Revision as of 05:18, 6 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6a4o is ON HOLD	+	The entry 6a4o is ON HOLD until Paper Publication

	Authors: Tushar, R., Kini, R.M., Koh, C.Y., Hosur, M.V.		Authors: Tushar, R., Kini, R.M., Koh, C.Y., Hosur, M.V.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Tushar, R]]		[[Category: Tushar, R]]
		+	[[Category: Hosur, M.V]]
	[[Category: Koh, C.Y]]		[[Category: Koh, C.Y]]
	[[Category: Kini, R.M]]		[[Category: Kini, R.M]]
-	[[Category: Hosur, M.V]]

OCA at 05:31, 4 July 2018

2018-07-04T05:31:23Z

←Older revision		Revision as of 05:31, 4 July 2018
Line 5:		Line 5:
	Authors: Tushar, R., Kini, R.M., Koh, C.Y., Hosur, M.V.		Authors: Tushar, R., Kini, R.M., Koh, C.Y., Hosur, M.V.

-	Description: HEWL crystals soaked in 2.5M GuHCl for 8 minutes.	+	Description: HEWL crystals soaked in 2.5M GuHCl for 20 minutes
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Tushar, R]]		[[Category: Tushar, R]]
-	[[Category: Hosur, M.V]]
	[[Category: Koh, C.Y]]		[[Category: Koh, C.Y]]
	[[Category: Kini, R.M]]		[[Category: Kini, R.M]]
		+	[[Category: Hosur, M.V]]

OCA: Protected "6a4o" [edit=sysop:move=sysop]

2018-06-27T03:54:25Z

Protected "6a4o" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:54, 27 June 2018

OCA: New page: '''Unreleased structure''' The entry 6a4o is ON HOLD Authors: Tushar, R., Kini, R.M., Koh, C.Y., Hosur, M.V. Description: HEWL crystals soaked in 2.5M GuHCl for 8 minutes. [[Category: ...

2018-06-27T03:54:24Z

New page: '''Unreleased structure''' The entry 6a4o is ON HOLD Authors: Tushar, R., Kini, R.M., Koh, C.Y., Hosur, M.V. Description: HEWL crystals soaked in 2.5M GuHCl for 8 minutes. [[Category: ...

New page

'''Unreleased structure'''

The entry 6a4o is ON HOLD

Authors: Tushar, R., Kini, R.M., Koh, C.Y., Hosur, M.V.

Description: HEWL crystals soaked in 2.5M GuHCl for 8 minutes.
[[Category: Unreleased Structures]]
[[Category: Tushar, R]]
[[Category: Hosur, M.V]]
[[Category: Koh, C.Y]]
[[Category: Kini, R.M]]