4glv - Revision history

OCA at 07:04, 26 October 2022

2022-10-26T07:04:50Z

←Older revision		Revision as of 07:04, 26 October 2022
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	==OBody AM3L09 bound to hen egg-white lysozyme==		==OBody AM3L09 bound to hen egg-white lysozyme==
-	<StructureSection load='4glv' size='340' side='right' caption='[[4glv]], [[Resolution\|resolution]] 2.57Å' scene=''>	+	<StructureSection load='4glv' size='340' side='right'caption='[[4glv]], [[Resolution\|resolution]] 2.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4glv]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_51768 Atcc 51768~~] and [~~http~~://en.wikipedia.org/wiki/~~Chick Chick~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GLV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4glv]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GLV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gla\|4gla]], [[4gn3\|4gn3]], [[4gn4\|4gn4]], [[4gn5\|4gn5]]</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=4glv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glv OCA], [https://pdbe.org/4glv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4glv RCSB], [https://www.ebi.ac.uk/pdbsum/4glv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4glv ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</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=4glv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glv OCA], [~~http~~://pdbe.org/4glv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4glv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4glv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4glv 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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 51768~~]]	+	[[Category: Gallus gallus]]
-	[[Category: ~~Chick~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lysozyme~~]]	+	[[Category: Pyrobaculum aerophilum]]
-	[[Category: Steemson~~, J D]]~~	+	[[Category: Steemson JD]]
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Engineered binding protein]]~~	+
-	~~[[Category: Enzyme inhibition]]~~	+
-	~~[[Category: Hydrolase-de novo protein complex]]~~	+
-	~~[[Category: Muraminidase]]~~	+
-	~~[[Category: Novel scaffold]]~~	+
-	~~[[Category: Ob-fold]]~~	+
-	~~[[Category: Protein-protein complex~~]]	+

OCA at 19:35, 4 August 2016

2016-08-04T19:35:09Z

←Older revision		Revision as of 19:35, 4 August 2016
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		+
	==OBody AM3L09 bound to hen egg-white lysozyme==		==OBody AM3L09 bound to hen egg-white lysozyme==
	<StructureSection load='4glv' size='340' side='right' caption='[[4glv]], [[Resolution\|resolution]] 2.57Å' scene=''>		<StructureSection load='4glv' size='340' side='right' caption='[[4glv]], [[Resolution\|resolution]] 2.57Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</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=4glv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4glv RCSB], [http://www.ebi.ac.uk/pdbsum/4glv PDBsum]</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=4glv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glv OCA], [http://pdbe.org/4glv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4glv RCSB], [http://www.ebi.ac.uk/pdbsum/4glv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4glv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4glv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 12:27, 25 December 2014

2014-12-25T12:27:40Z

←Older revision		Revision as of 12:27, 25 December 2014
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-	~~{{STRUCTURE_4glv\| PDB=4glv \| SCENE= }}~~	+	==OBody AM3L09 bound to hen egg-white lysozyme==
-	===OBody AM3L09 bound to hen egg-white lysozyme===	+	<StructureSection load='4glv' size='340' side='right' caption='[[4glv]], [[Resolution\|resolution]] 2.57Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24465865}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4glv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768] and [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GLV FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gla\|4gla]], [[4gn3\|4gn3]], [[4gn4\|4gn4]], [[4gn5\|4gn5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</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=4glv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4glv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4glv RCSB], [http://www.ebi.ac.uk/pdbsum/4glv PDBsum]</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>		[[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 ==
		+	The OB-fold is a small, versatile single-domain protein binding module that occurs in all forms of life, where it binds protein, carbohydrate, nucleic acid and small-molecule ligands. We have exploited this natural plasticity to engineer a new class of non-immunoglobulin alternatives to antibodies with unique structural and biophysical characteristics. We present here the engineering of the OB-fold anticodon recognition domain from aspartyl tRNA synthetase taken from the thermophile Pyrobaculum aerophilum. For this single-domain scaffold we have coined the term OBody. Starting from a naive combinatorial library, we engineered an OBody with 3 nM affinity for hen egg-white lysozyme, by optimising the affinity of a naive OBody 11,700-fold over several affinity maturation steps, using phage display. At each maturation step a crystal structure of the engineered OBody in complex with hen egg-white lysozyme was determined, showing binding elements in atomic detail. These structures have given us an unprecedented insight into the directed evolution of affinity for a single antigen on the molecular scale. The engineered OBodies retain the high thermal stability of the parental OB-fold despite mutation of up to 22% of their residues. They can be expressed in soluble form and also purified from bacteria at high yields. They also lack disulfide bonds. These data demonstrate the potential of OBodies as a new scaffold for the engineering of specific binding reagents and provide a platform for further development of future OBody-based applications.
		+
		+	Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold.,Steemson JD, Baake M, Rakonjac J, Arcus VL, Liddament MT PLoS One. 2014 Jan 20;9(1):e86050. doi: 10.1371/journal.pone.0086050. eCollection, 2014 Jan 20. PMID:24465865<ref>PMID:24465865</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4glv]] is~~ a ~~8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Atcc_51768 Atcc 51768] and [http://en~~.~~wikipedia.org~~/~~wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLV OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024465865</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Atcc 51768]]		[[Category: Atcc 51768]]
	[[Category: Chick]]		[[Category: Chick]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Steemson, J D.]]	+	[[Category: Steemson, J D]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Engineered binding protein]]		[[Category: Engineered binding protein]]

OCA at 03:22, 13 February 2014

2014-02-13T03:22:28Z

←Older revision		Revision as of 03:22, 13 February 2014
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	{{STRUCTURE_4glv\| PDB=4glv \| SCENE= }}		{{STRUCTURE_4glv\| PDB=4glv \| SCENE= }}
	===OBody AM3L09 bound to hen egg-white lysozyme===		===OBody AM3L09 bound to hen egg-white lysozyme===
		+	{{ABSTRACT_PUBMED_24465865}}

	==Function==		==Function==
Line 6:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4glv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Gallus_gallus Gallus gallus~~] and [http://en.wikipedia.org/wiki/~~Pyrobaculum_aerophilum Pyrobaculum aerophilum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLV OCA].	+	[[4glv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768] and [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLV OCA].

	==Reference==		==Reference==
-	<references group="xtra"/><references/>	+	<ref group="xtra">PMID:024465865</ref><references group="xtra"/><references/>
-	[[Category: ~~Gallus gallus~~]]	+	[[Category: Atcc 51768]]
		+	[[Category: Chick]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
-	[[Category: Pyrobaculum aerophilum]]
	[[Category: Steemson, J D.]]		[[Category: Steemson, J D.]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]

OCA at 08:32, 21 August 2013

2013-08-21T08:32:52Z

←Older revision		Revision as of 08:32, 21 August 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4glv\| PDB=4glv \| SCENE= }}
		+	===OBody AM3L09 bound to hen egg-white lysozyme===

-	~~The entry 4glv is ON HOLD~~ ~~until Paper Publication~~	+	==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>

-	~~Authors~~: ~~Steemson, J~~.D.	+	==About this Structure==
		+	[[4glv]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GLV OCA].

-	~~Description~~: ~~OBody AM3L09 bound to hen egg~~-~~white lysozyme~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Gallus gallus]]
		+	[[Category: Lysozyme]]
		+	[[Category: Pyrobaculum aerophilum]]
		+	[[Category: Steemson, J D.]]
		+	[[Category: Beta barrel]]
		+	[[Category: Engineered binding protein]]
		+	[[Category: Enzyme inhibition]]
		+	[[Category: Hydrolase-de novo protein complex]]
		+	[[Category: Muraminidase]]
		+	[[Category: Novel scaffold]]
		+	[[Category: Ob-fold]]
		+	[[Category: Protein-protein complex]]

OCA at 07:05, 24 October 2012

2012-10-24T07:05:23Z

←Older revision		Revision as of 07:05, 24 October 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4glv is ON HOLD	+	The entry 4glv is ON HOLD until Paper Publication

	Authors: Steemson, J.D.		Authors: Steemson, J.D.

	Description: OBody AM3L09 bound to hen egg-white lysozyme		Description: OBody AM3L09 bound to hen egg-white lysozyme

OCA: Protected "4glv" [edit=sysop:move=sysop]

2012-08-22T05:37:14Z

Protected "4glv" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:37, 22 August 2012

OCA: New page: '''Unreleased structure''' The entry 4glv is ON HOLD Authors: Steemson, J.D. Description: OBody AM3L09 bound to hen egg-white lysozyme

2012-08-22T05:37:13Z

New page: '''Unreleased structure''' The entry 4glv is ON HOLD Authors: Steemson, J.D. Description: OBody AM3L09 bound to hen egg-white lysozyme

New page

'''Unreleased structure'''

The entry 4glv is ON HOLD

Authors: Steemson, J.D.

Description: OBody AM3L09 bound to hen egg-white lysozyme