4ink - Revision history

OCA at 15:27, 20 September 2023

2023-09-20T15:27:04Z

←Older revision		Revision as of 15:27, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ink]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4INK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4INK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ink]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4INK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4INK FirstGlance]. <br>
-	</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=4ink FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ink OCA], [https://pdbe.org/4ink PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ink RCSB], [https://www.ebi.ac.uk/pdbsum/4ink PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ink ProSAT]</span></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]] 1.56Å</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=4ink FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ink OCA], [https://pdbe.org/4ink PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ink RCSB], [https://www.ebi.ac.uk/pdbsum/4ink PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ink ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:58, 16 November 2022

2022-11-16T20:58:01Z

←Older revision		Revision as of 20:58, 16 November 2022
Line 1:		Line 1:

	==Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution==		==Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution==
-	<StructureSection load='4ink' size='340' side='right' caption='[[4ink]], [[Resolution\|resolution]] 1.56Å' scene=''>	+	<StructureSection load='4ink' size='340' side='right'caption='[[4ink]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ink]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staa8 Staa8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4INK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4INK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ink]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4INK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4INK FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4inl\|4inl]]</td></tr>~~	+	</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=4ink FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ink OCA], [https://pdbe.org/4ink PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ink RCSB], [https://www.ebi.ac.uk/pdbsum/4ink PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ink ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAOUHSC_01938, splD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</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=4ink FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ink OCA], [~~http~~://pdbe.org/4ink PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ink RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ink PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ink ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SPLD_STAA8 SPLD_STAA8]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staa8~~]]	+	[[Category: Large Structures]]
-	[[Category: Cichon, P]]	+	[[Category: Staphylococcus aureus subsp. aureus NCTC 8325]]
-	[[Category: Daugherty~~, P S~~]]	+	[[Category: Cichon P]]
-	[[Category: Dubin, A]]	+	[[Category: Daugherty PS]]
-	[[Category: Dubin, G]]	+	[[Category: Dubin A]]
-	[[Category: Jabaiah, A]]	+	[[Category: Dubin G]]
-	[[Category: Kalinska, M]]	+	[[Category: Jabaiah A]]
-	[[Category: Lesner, A]]	+	[[Category: Kalinska M]]
-	[[Category: Markiewicz, M]]	+	[[Category: Lesner A]]
-	[[Category: Potempa, J]]	+	[[Category: Markiewicz M]]
-	[[Category: Rolka, K]]	+	[[Category: Potempa J]]
-	[[Category: Stec-Niemczyk, J]]	+	[[Category: Rolka K]]
-	[[Category: Stennicke~~, H R~~]]	+	[[Category: Stec-Niemczyk J]]
-	[[Category: Wladyka, B]]	+	[[Category: Stennicke HR]]
-	[[Category: Wysocka, M]]	+	[[Category: Wladyka B]]
-	[[Category: Zdzalik, M]]	+	[[Category: Wysocka M]]
-	~~[[Category: Chymotrypsin-like protease]]~~	+	[[Category: Zdzalik M]]
-	~~[[Category: Extracellular staphylococcal protease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Serine endopeptidase~~]]	+

OCA at 18:18, 11 August 2016

2016-08-11T18:18:26Z

←Older revision		Revision as of 18:18, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution==		==Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution==
	<StructureSection load='4ink' size='340' side='right' caption='[[4ink]], [[Resolution\|resolution]] 1.56Å' scene=''>		<StructureSection load='4ink' size='340' side='right' caption='[[4ink]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ink]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus_subsp._aureus_nctc_8325 Staphylococcus aureus subsp. aureus nctc 8325~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4INK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4INK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ink]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staa8 Staa8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4INK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4INK FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4inl\|4inl]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4inl\|4inl]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAOUHSC_01938, splD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 ~~Staphylococcus aureus subsp. aureus NCTC 8325~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAOUHSC_01938, splD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</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=4ink FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ink OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ink RCSB], [http://www.ebi.ac.uk/pdbsum/4ink 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=4ink FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ink OCA], [http://pdbe.org/4ink PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ink RCSB], [http://www.ebi.ac.uk/pdbsum/4ink PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ink ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4ink" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staphylococcus aureus subsp. aureus nctc 8325~~]]	+	[[Category: Staa8]]
	[[Category: Cichon, P]]		[[Category: Cichon, P]]
	[[Category: Daugherty, P S]]		[[Category: Daugherty, P S]]

OCA at 09:19, 25 January 2015

2015-01-25T09:19:31Z

←Older revision		Revision as of 09:19, 25 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4ink\| PDB=4ink \| SCENE= }}~~	+	==Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution==
-	===Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution===	+	<StructureSection load='4ink' size='340' side='right' caption='[[4ink]], [[Resolution\|resolution]] 1.56Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24130791}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ink]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_nctc_8325 Staphylococcus aureus subsp. aureus nctc 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4INK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4INK FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4inl\|4inl]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAOUHSC_01938, splD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 Staphylococcus aureus subsp. aureus NCTC 8325])</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=4ink FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ink OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ink RCSB], [http://www.ebi.ac.uk/pdbsum/4ink PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Staphylococcus aureus is a dangerous human pathogen. A number of the proteins secreted by this bacterium are implicated in its virulence, but many of the components of its secretome are poorly characterized. Strains of S. aureus can produce up to six homologous extracellular serine proteases grouped in a single spl operon. Although the SplA, SplB, and SplC proteases have been thoroughly characterized, the properties of the other three enzymes have not yet been investigated. Here, we describe the biochemical and structural characteristics of the SplD protease. The active enzyme was produced in an Escherichia coli recombinant system and purified to homogeneity. P1 substrate specificity was determined using a combinatorial library of synthetic peptide substrates showing exclusive preference for threonine, serine, leucine, isoleucine, alanine, and valine. To further determine the specificity of SplD, we used high-throughput synthetic peptide and cell surface protein display methods. The results not only confirmed SplD preference for a P1 residue, but also provided insight into the specificity of individual primed- and non-primed substrate-binding subsites. The analyses revealed a surprisingly narrow specificity of the protease, which recognized five consecutive residues (P4-P3-P2-P1-P1') with a consensus motif of R-(Y/W)-(P/L)-(T/L/I/V) downward arrowS. To understand the molecular basis of the strict substrate specificity, we crystallized the enzyme in two different conditions, and refined the structures at resolutions of 1.56 A and 2.1 A. Molecular modeling and mutagenesis studies allowed us to define a consensus model of substrate binding, and illustrated the molecular mechanism of protease specificity.

-	~~==About this Structure==~~	+	Biochemical and Structural Characterization of SplD Protease from Staphylococcus aureus.,Zdzalik M, Kalinska M, Wysocka M, Stec-Niemczyk J, Cichon P, Stach N, Gruba N, Stennicke HR, Jabaiah A, Markiewicz M, Kedracka-Krok S, Wladyka B, Daugherty PS, Lesner A, Rolka K, Dubin A, Potempa J, Dubin G PLoS One. 2013 Oct 9;8(10):e76812. doi: 10.1371/journal.pone.0076812. PMID:24130791<ref>PMID:24130791</ref>
-	~~[[4ink]] is a 1 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_nctc_8325~~ Staphylococcus aureus ~~subsp~~. ~~aureus nctc 8325]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4INK OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024130791</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Staphylococcus aureus subsp. aureus nctc 8325]]		[[Category: Staphylococcus aureus subsp. aureus nctc 8325]]
-	[[Category: Cichon, P.]]	+	[[Category: Cichon, P]]
-	[[Category: Daugherty, P S.]]	+	[[Category: Daugherty, P S]]
-	[[Category: Dubin, A.]]	+	[[Category: Dubin, A]]
-	[[Category: Dubin, G.]]	+	[[Category: Dubin, G]]
-	[[Category: Jabaiah, A.]]	+	[[Category: Jabaiah, A]]
-	[[Category: Kalinska, M.]]	+	[[Category: Kalinska, M]]
-	[[Category: Lesner, A.]]	+	[[Category: Lesner, A]]
-	[[Category: Markiewicz, M.]]	+	[[Category: Markiewicz, M]]
-	[[Category: Potempa, J.]]	+	[[Category: Potempa, J]]
-	[[Category: Rolka, K.]]	+	[[Category: Rolka, K]]
-	[[Category: Stec-Niemczyk, J.]]	+	[[Category: Stec-Niemczyk, J]]
-	[[Category: Stennicke, H R.]]	+	[[Category: Stennicke, H R]]
-	[[Category: Wladyka, B.]]	+	[[Category: Wladyka, B]]
-	[[Category: Wysocka, M.]]	+	[[Category: Wysocka, M]]
-	[[Category: Zdzalik, M.]]	+	[[Category: Zdzalik, M]]
	[[Category: Chymotrypsin-like protease]]		[[Category: Chymotrypsin-like protease]]
	[[Category: Extracellular staphylococcal protease]]		[[Category: Extracellular staphylococcal protease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Serine endopeptidase]]		[[Category: Serine endopeptidase]]

OCA at 09:36, 30 October 2013

2013-10-30T09:36:13Z

←Older revision		Revision as of 09:36, 30 October 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4ink\| PDB=4ink \| SCENE= }}
		+	===Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution===
		+	{{ABSTRACT_PUBMED_24130791}}

-	~~The entry~~ 4ink is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4ink]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_nctc_8325 Staphylococcus aureus subsp. aureus nctc 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4INK OCA].

-	~~Authors~~: ~~Zdzalik, M~~.~~, Kalinska, M.,~~ Cichon, P., ~~Wysocka, M~~., ~~Stec-Niemczyk, J~~., ~~Stennicke, H.R~~., Jabaiah, A.~~, Markiewicz~~, M., ~~Wladyka, B~~., ~~Daugherty, P.S~~., ~~Lesner, A~~., Rolka, K., ~~Dubin~~, A., ~~Potempa~~, J., ~~Dubin, G~~.	+	==Reference==
-		+	<ref group="xtra">PMID:024130791</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure of SplD~~ protease ~~from Staphylococcus aureus at 1.56 A resolution~~	+	[[Category: Staphylococcus aureus subsp. aureus nctc 8325]]
		+	[[Category: Cichon, P.]]
		+	[[Category: Daugherty, P S.]]
		+	[[Category: Dubin, A.]]
		+	[[Category: Dubin, G.]]
		+	[[Category: Jabaiah, A.]]
		+	[[Category: Kalinska, M.]]
		+	[[Category: Lesner, A.]]
		+	[[Category: Markiewicz, M.]]
		+	[[Category: Potempa, J.]]
		+	[[Category: Rolka, K.]]
		+	[[Category: Stec-Niemczyk, J.]]
		+	[[Category: Stennicke, H R.]]
		+	[[Category: Wladyka, B.]]
		+	[[Category: Wysocka, M.]]
		+	[[Category: Zdzalik, M.]]
		+	[[Category: Chymotrypsin-like protease]]
		+	[[Category: Extracellular staphylococcal protease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Serine endopeptidase]]

OCA at 11:11, 23 January 2013

2013-01-23T11:11:52Z

←Older revision		Revision as of 11:11, 23 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Zdzalik, M., Cichon, P., Stec-Niemczyk, J., Potempa, J., Dubin, G.	+	Authors: Zdzalik, M., Kalinska, M., Cichon, P., Wysocka, M., Stec-Niemczyk, J., Stennicke, H.R., Jabaiah, A., Markiewicz, M., Wladyka, B., Daugherty, P.S., Lesner, A., Rolka, K., Dubin, A., Potempa, J., Dubin, G.

-	Description: Crystal structure of ~~Spld~~ protease from Staphylococcus aureus at 1.56 A resolution	+	Description: Crystal structure of SplD protease from Staphylococcus aureus at 1.56 A resolution

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

2013-01-16T08:26:47Z

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

←Older revision

Revision as of 08:26, 16 January 2013

OCA: New page: '''Unreleased structure''' The entry 4ink is ON HOLD Authors: Zdzalik, M., Cichon, P., Stec-Niemczyk, J., Potempa, J., Dubin, G. Description: Crystal structure of Spld protease from St...

2013-01-16T08:26:46Z

New page: '''Unreleased structure''' The entry 4ink is ON HOLD Authors: Zdzalik, M., Cichon, P., Stec-Niemczyk, J., Potempa, J., Dubin, G. Description: Crystal structure of Spld protease from St...

New page

'''Unreleased structure'''

The entry 4ink is ON HOLD

Authors: Zdzalik, M., Cichon, P., Stec-Niemczyk, J., Potempa, J., Dubin, G.

Description: Crystal structure of Spld protease from Staphylococcus aureus at 1.56 A resolution