5zkm - Revision history

OCA at 08:59, 22 November 2023

2023-11-22T08:59:08Z

←Older revision		Revision as of 08:59, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5zkm' size='340' side='right'caption='[[5zkm]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5zkm' size='340' side='right'caption='[[5zkm]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zkm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strpn Strpn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zkm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4] 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=5ZKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZKM FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SP_0782 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=170187 STRPN])~~</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]] 1.65Å</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=5zkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkm OCA], [~~http~~://pdbe.org/5zkm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zkm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zkm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkm 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=5zkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkm OCA], [https://pdbe.org/5zkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zkm RCSB], [https://www.ebi.ac.uk/pdbsum/5zkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H2UPA7_STRPN A0A0H2UPA7_STRPN]
	<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: ~~Strpn~~]]	+	[[Category: Streptococcus pneumoniae TIGR4]]
-	[[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

2019-11-27T08:14:26Z

←Older revision		Revision as of 08:14, 27 November 2019
Line 3:		Line 3:
	<StructureSection load='5zkm' size='340' side='right'caption='[[5zkm]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5zkm' size='340' side='right'caption='[[5zkm]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zkm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZKM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zkm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strpn Strpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZKM 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=5zkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkm OCA], [http://pdbe.org/5zkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkm RCSB], [http://www.ebi.ac.uk/pdbsum/5zkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkm ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SP_0782 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])</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=5zkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkm OCA], [http://pdbe.org/5zkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkm RCSB], [http://www.ebi.ac.uk/pdbsum/5zkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkm 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 5zkm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Strpn]]
	[[Category: Gong, P]]		[[Category: Gong, P]]
	[[Category: Li, S]]		[[Category: Li, S]]

OCA at 06:30, 27 March 2019

2019-03-27T06:30:52Z

←Older revision		Revision as of 06:30, 27 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5zkm is ON HOLD until Paper Publication~~	+	==Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA TCTTCC==
-		+	<StructureSection load='5zkm' size='340' side='right'caption='[[5zkm]], [[Resolution\|resolution]] 1.65Å' scene=''>
-	~~Authors: Lu, G., Li, S., Zhu, J., Yang, Y., Gong, P.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zkm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZKM FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA TCTTCC	+	</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=5zkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkm OCA], [http://pdbe.org/5zkm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkm RCSB], [http://www.ebi.ac.uk/pdbsum/5zkm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkm 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 03:49, 30 May 2018

2018-05-30T03:49:42Z

←Older revision		Revision as of 03:49, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zkm is ON HOLD	+	The entry 5zkm 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 "5zkm" [edit=sysop:move=sysop]

2018-04-04T04:31:50Z

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

←Older revision

Revision as of 04:31, 4 April 2018

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

2018-04-04T04:31:48Z

New page: '''Unreleased structure''' The entry 5zkm 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 5zkm 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 TCTTCC
[[Category: Unreleased Structures]]
[[Category: Li, S]]
[[Category: Gong, P]]
[[Category: Zhu, J]]
[[Category: Yang, Y]]
[[Category: Lu, G]]