5zkl - Revision history

OCA at 08:59, 22 November 2023

OCA — Wed, 22 Nov 2023 08:59:02 GMT

←Older revision		Revision as of 08:59, 22 November 2023
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	<StructureSection load='5zkl' size='340' side='right'caption='[[5zkl]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5zkl' size='340' side='right'caption='[[5zkl]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zkl]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strr6 Strr6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zkl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZKL FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~spr0690~~, ~~sp_0782 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=171101 STRR6])~~</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]] 1.951Å</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=5zkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkl OCA], [~~http~~://pdbe.org/5zkl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zkl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zkl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkl 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=5zkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkl OCA], [https://pdbe.org/5zkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zkl RCSB], [https://www.ebi.ac.uk/pdbsum/5zkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8DQG2_STRR6 Q8DQG2_STRR6]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Strr6~~]]	+	[[Category: Streptococcus pneumoniae R6]]
-	[[Category: Gong, P]]	+	[[Category: Synthetic construct]]
-	[[Category: Li, S]]	+	[[Category: Gong P]]
-	[[Category: Lu, G]]	+	[[Category: Li S]]
-	[[Category: Yang, Y]]	+	[[Category: Lu G]]
-	[[Category: Zhu, J]]	+	[[Category: Yang Y]]
-	~~[[Category: Protein-dna complex]]~~	+	[[Category: Zhu J]]
-	~~[[Category: Unknown function-dna complex~~]]	+

OCA at 08:14, 27 November 2019

OCA — Wed, 27 Nov 2019 08:14:26 GMT

←Older revision		Revision as of 08:14, 27 November 2019
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	<StructureSection load='5zkl' size='340' side='right'caption='[[5zkl]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5zkl' size='340' side='right'caption='[[5zkl]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zkl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zkl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZKL FirstGlance]. <br>
-	</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=5zkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkl OCA], [http://pdbe.org/5zkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkl RCSB], [http://www.ebi.ac.uk/pdbsum/5zkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkl ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spr0690, sp_0782 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</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=5zkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkl OCA], [http://pdbe.org/5zkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkl RCSB], [http://www.ebi.ac.uk/pdbsum/5zkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkl ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	SP_0782 from Streptococcus pneumoniae is a dimeric protein that potentially binds with single-stranded DNA (ssDNA) in a manner similar to human PC4, the prototype of PC4-like proteins, which plays roles in transcription and maintenance of genome stability. In a previous NMR study, SP_0782 exhibited an ssDNA-binding property different from YdbC, a prokaryotic PC4-like protein from Lactococcus lactis, but the underlying mechanism remains unclear. Here, we show that although SP_0782 adopts an overall fold similar to those of PC4 and YdbC, the ssDNA length occupied by SP_0782 is shorter than those occupied by PC4 and YdbC. SP_0782 exhibits varied binding patterns for different lengths of ssDNA, and tends to form large complexes with ssDNA in a potential high-density binding manner. The structures of SP_0782 complexed with different ssDNAs reveal that the varied binding patterns are associated with distinct capture of nucleotides in two major DNA-binding regions of SP_0782. Moreover, a comparison of known structures of PC4-like proteins complexed with ssDNA reveals a divergence in the binding interface between prokaryotic and eukaryotic PC4-like proteins. This study provides insights into the ssDNA-binding mechanism of PC4-like proteins, and benefits further study regarding the biological function of SP_0782, probably in DNA protection and natural transformation.
		+
		+	Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins.,Li S, Lu G, Fang X, Ramelot TA, Kennedy MA, Zhou X, Gong P, Zhang X, Liu M, Zhu J, Yang Y Nucleic Acids Res. 2019 Nov 12. pii: 5622711. doi: 10.1093/nar/gkz1045. PMID:31713614<ref>PMID:31713614</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zkl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Strr6]]
	[[Category: Gong, P]]		[[Category: Gong, P]]
	[[Category: Li, S]]		[[Category: Li, S]]

OCA at 06:30, 27 March 2019

OCA — Wed, 27 Mar 2019 06:30:50 GMT

←Older revision		Revision as of 06:30, 27 March 2019
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-	'''Unreleased structure'''

-	~~The entry 5zkl is ON HOLD until Paper Publication~~	+	==Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA dT12==
-		+	<StructureSection load='5zkl' size='340' side='right'caption='[[5zkl]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~Authors: Lu, G., Li, S., Zhu, J., Yang, Y., Gong, P.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zkl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZKL FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA dT12	+	</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=5zkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkl OCA], [http://pdbe.org/5zkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkl RCSB], [http://www.ebi.ac.uk/pdbsum/5zkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkl ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gong, P]]
	[[Category: Li, S]]		[[Category: Li, S]]
-	[[Category: ~~Gong~~, P]]	+	[[Category: Lu, G]]
		+	[[Category: Yang, Y]]
	[[Category: Zhu, J]]		[[Category: Zhu, J]]
-	[[Category: ~~Yang, Y~~]]	+	[[Category: Protein-dna complex]]
-	[[Category: ~~Lu, G~~]]	+	[[Category: Unknown function-dna complex]]

OCA at 04:06, 6 June 2018

OCA — Wed, 06 Jun 2018 04:06:15 GMT

←Older revision		Revision as of 04:06, 6 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zkl is ON HOLD	+	The entry 5zkl is ON HOLD until Paper Publication

	Authors: Lu, G., Li, S., Zhu, J., Yang, Y., Gong, P.		Authors: Lu, G., Li, S., Zhu, J., Yang, Y., Gong, P.

OCA: Protected "5zkl" [edit=sysop:move=sysop]

OCA — Wed, 04 Apr 2018 04:31:44 GMT

Protected "5zkl" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:31, 4 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zkl is ON HOLD Authors: Lu, G., Li, S., Zhu, J., Yang, Y., Gong, P. Description: Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7...

OCA — Wed, 04 Apr 2018 04:31:43 GMT

New page: '''Unreleased structure''' The entry 5zkl is ON HOLD Authors: Lu, G., Li, S., Zhu, J., Yang, Y., Gong, P. Description: Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7...

New page

'''Unreleased structure'''

The entry 5zkl is ON HOLD

Authors: Lu, G., Li, S., Zhu, J., Yang, Y., Gong, P.

Description: Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA dT12
[[Category: Unreleased Structures]]
[[Category: Li, S]]
[[Category: Gong, P]]
[[Category: Zhu, J]]
[[Category: Yang, Y]]
[[Category: Lu, G]]