6ilu - Revision history

OCA at 10:33, 27 March 2024

OCA — Wed, 27 Mar 2024 10:33:50 GMT

←Older revision		Revision as of 10:33, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6ilu' size='340' side='right'caption='[[6ilu]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6ilu' size='340' side='right'caption='[[6ilu]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ilu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacillus_cereus_phage_pbc5~~ Bacillus ~~cereus~~ phage ~~pbc5~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ILU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ilu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_phage_PBC5 Bacillus phage PBC5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ILU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.601Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PBC5_032 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1675030 Bacillus cereus phage PBC5])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6ilu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ilu OCA], [~~http~~://pdbe.org/6ilu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ilu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ilu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ilu 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=6ilu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ilu OCA], [https://pdbe.org/6ilu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ilu RCSB], [https://www.ebi.ac.uk/pdbsum/6ilu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ilu ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A218KCJ1_9CAUD A0A218KCJ1_9CAUD]
-	Phage endolysins are hydrolytic enzymes that cleave the bacterial cell wall during the lytic cycle. We isolated the bacteriophage PBC5 against Bacillus cereus, a major foodborne pathogen, and describe the molecular interaction between endolysin LysPBC5 and the host peptidoglycan structure. LysPBC5 has an N-terminal glycoside hydrolase 25 domain, and a C-terminal cell-wall binding domain (CBD) that is critical for specific cell-wall recognition and lysis. The crystal and solution structures of CBDs reveal tandem SH3b domains that are tightly engaged with each other. The CBD binds to the peptidoglycan in a bidentate manner via distal beta sheet motifs with pseudo 2-fold symmetry, which can explain its high affinity and host specificity. The CBD primarily interacts with the glycan strand of the peptidoglycan layer instead of the peptide crosslink, implicating the tertiary structure of peptidoglycan as the recognition motif of endolysins.	+
-		+
-	~~Structural Basis for Cell-Wall Recognition by Bacteriophage PBC5 Endolysin.,Lee KO, Kong M, Kim I, Bai J, Cha S, Kim B, Ryu KS, Ryu S, Suh JY Structure. 2019 Sep 3;27(9)~~:~~1355-1365.e4. doi: 10.1016~~/~~j.str.2019.07.001. Epub, 2019 Jul 25. PMID:31353242<ref>PMID:31353242<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6ilu" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
-	*[[Lysin\|Lysin]]	+	*[[Lysin 3D structures\|Lysin 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~cereus~~ phage ~~pbc5~~]]	+	[[Category: Bacillus phage PBC5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bae~~, J W~~]]	+	[[Category: Bae JW]]
-	[[Category: Kim~~, I T~~]]	+	[[Category: Kim IT]]
-	[[Category: Kong~~, M S~~]]	+	[[Category: Kong MS]]
-	[[Category: Lee~~, K O~~]]	+	[[Category: Lee KO]]
-	[[Category: Ryu~~, K S~~]]	+	[[Category: Ryu KS]]
-	[[Category: Ryu, S]]	+	[[Category: Ryu S]]
-	[[Category: Suh~~, J Y]]~~	+	[[Category: Suh JY]]
-	~~[[Category: Cell-wall binding]]~~	+
-	~~[[Category: Endolysin]]~~	+
-	~~[[Category: Pbc5]]~~	+
-	~~[[Category: Sh3b]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 04:37, 13 February 2020

OCA — Thu, 13 Feb 2020 04:37:17 GMT

←Older revision		Revision as of 04:37, 13 February 2020
Line 8:		Line 8:
	<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=6ilu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ilu OCA], [http://pdbe.org/6ilu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ilu RCSB], [http://www.ebi.ac.uk/pdbsum/6ilu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ilu 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=6ilu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ilu OCA], [http://pdbe.org/6ilu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ilu RCSB], [http://www.ebi.ac.uk/pdbsum/6ilu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ilu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phage endolysins are hydrolytic enzymes that cleave the bacterial cell wall during the lytic cycle. We isolated the bacteriophage PBC5 against Bacillus cereus, a major foodborne pathogen, and describe the molecular interaction between endolysin LysPBC5 and the host peptidoglycan structure. LysPBC5 has an N-terminal glycoside hydrolase 25 domain, and a C-terminal cell-wall binding domain (CBD) that is critical for specific cell-wall recognition and lysis. The crystal and solution structures of CBDs reveal tandem SH3b domains that are tightly engaged with each other. The CBD binds to the peptidoglycan in a bidentate manner via distal beta sheet motifs with pseudo 2-fold symmetry, which can explain its high affinity and host specificity. The CBD primarily interacts with the glycan strand of the peptidoglycan layer instead of the peptide crosslink, implicating the tertiary structure of peptidoglycan as the recognition motif of endolysins.
		+
		+	Structural Basis for Cell-Wall Recognition by Bacteriophage PBC5 Endolysin.,Lee KO, Kong M, Kim I, Bai J, Cha S, Kim B, Ryu KS, Ryu S, Suh JY Structure. 2019 Sep 3;27(9):1355-1365.e4. doi: 10.1016/j.str.2019.07.001. Epub, 2019 Jul 25. PMID:31353242<ref>PMID:31353242</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ilu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysin\|Lysin]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:15, 7 August 2019

OCA — Wed, 07 Aug 2019 06:15:45 GMT

←Older revision		Revision as of 06:15, 7 August 2019
Line 3:		Line 3:
	<StructureSection load='6ilu' size='340' side='right'caption='[[6ilu]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6ilu' size='340' side='right'caption='[[6ilu]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ilu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ILU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ilu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus_phage_pbc5 Bacillus cereus phage pbc5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ILU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBC5_032 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1675030 Bacillus cereus phage PBC5])</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=6ilu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ilu OCA], [http://pdbe.org/6ilu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ilu RCSB], [http://www.ebi.ac.uk/pdbsum/6ilu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ilu 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=6ilu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ilu OCA], [http://pdbe.org/6ilu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ilu RCSB], [http://www.ebi.ac.uk/pdbsum/6ilu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ilu ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus cereus phage pbc5]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bae, J W]]		[[Category: Bae, J W]]

OCA at 06:17, 31 July 2019

OCA — Wed, 31 Jul 2019 06:17:43 GMT

←Older revision		Revision as of 06:17, 31 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ilu ~~is ON HOLD until Paper Publication~~	+	==Endolysin LysPBC5 CBD==
-		+	<StructureSection load='6ilu' size='340' side='right'caption='[[6ilu]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~: ~~Suh, J~~.Y.~~, Ryu, K~~.S., ~~Ryu~~, S., ~~Lee, K~~.O., ~~Kong~~, M.S., ~~Bae, J~~.W., ~~Kim, I~~.T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ilu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ILU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ILU FirstGlance]. <br>
-	~~Description: Endolysin LysPBC5 CBD~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6ilu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ilu OCA], [http://pdbe.org/6ilu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ilu RCSB], [http://www.ebi.ac.uk/pdbsum/6ilu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ilu ProSAT]</span></td></tr>
-	[[Category: Bae, J.W]]	+	</table>
-	[[Category: Kim, I.T]]	+	__TOC__
-	[[Category: ~~Lee~~, ~~K.O~~]]	+	</StructureSection>
-	[[Category: ~~Ryu~~, K.S]]	+	[[Category: Large Structures]]
-	[[Category: ~~Suh~~, ~~J.Y~~]]	+	[[Category: Bae, J W]]
		+	[[Category: Kim, I T]]
		+	[[Category: Kong, M S]]
		+	[[Category: Lee, K O]]
		+	[[Category: Ryu, K S]]
	[[Category: Ryu, S]]		[[Category: Ryu, S]]
-	[[Category: ~~Kong~~, ~~M.S~~]]	+	[[Category: Suh, J Y]]
		+	[[Category: Cell-wall binding]]
		+	[[Category: Endolysin]]
		+	[[Category: Pbc5]]
		+	[[Category: Sh3b]]
		+	[[Category: Sugar binding protein]]

OCA at 04:47, 2 January 2019

OCA — Wed, 02 Jan 2019 04:47:25 GMT

←Older revision		Revision as of 04:47, 2 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Suh, J.Y., Ryu, K.S., Ryu, S., Lee, K.O., Kong, M.S., Bae, J.W., Kim, I.T.		Authors: Suh, J.Y., Ryu, K.S., Ryu, S., Lee, K.O., Kong, M.S., Bae, J.W., Kim, I.T.

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

OCA — Wed, 24 Oct 2018 04:26:37 GMT

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

←Older revision

Revision as of 04:26, 24 October 2018

OCA: New page: '''Unreleased structure''' The entry 6ilu is ON HOLD Authors: Suh, J.Y., Ryu, K.S., Ryu, S., Lee, K.O., Kong, M.S., Bae, J.W., Kim, I.T. Description: Endolysin LysPBC5 CBD [[Category: ...

OCA — Wed, 24 Oct 2018 04:26:35 GMT

New page: '''Unreleased structure''' The entry 6ilu is ON HOLD Authors: Suh, J.Y., Ryu, K.S., Ryu, S., Lee, K.O., Kong, M.S., Bae, J.W., Kim, I.T. Description: Endolysin LysPBC5 CBD [[Category: ...

New page

'''Unreleased structure'''

The entry 6ilu is ON HOLD

Authors: Suh, J.Y., Ryu, K.S., Ryu, S., Lee, K.O., Kong, M.S., Bae, J.W., Kim, I.T.

Description: Endolysin LysPBC5 CBD
[[Category: Unreleased Structures]]
[[Category: Bae, J.W]]
[[Category: Kim, I.T]]
[[Category: Lee, K.O]]
[[Category: Ryu, K.S]]
[[Category: Suh, J.Y]]
[[Category: Ryu, S]]
[[Category: Kong, M.S]]