4mz9 - Revision history

OCA at 16:45, 20 September 2023

2023-09-20T16:45:07Z

←Older revision		Revision as of 16:45, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4mz9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MZ9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4mz9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MZ9 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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [https://pdbe.org/4mz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [https://www.ebi.ac.uk/pdbsum/4mz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mz9 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]] 2.2Å</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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [https://pdbe.org/4mz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [https://www.ebi.ac.uk/pdbsum/4mz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mz9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 10:21, 28 December 2022

2022-12-28T10:21:43Z

←Older revision		Revision as of 10:21, 28 December 2022
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	==Revised structure of E. coli SSB==		==Revised structure of E. coli SSB==
-	<StructureSection load='4mz9' size='340' side='right' caption='[[4mz9]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4mz9' size='340' side='right'caption='[[4mz9]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4mz9]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZ9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MZ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4mz9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MZ9 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qvc\|1qvc]], [[1sru\|1sru]], [[1eyg\|1eyg]]</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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [https://pdbe.org/4mz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [https://www.ebi.ac.uk/pdbsum/4mz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mz9 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4059, exrB, JW4020, lexC, ssb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [~~http~~://pdbe.org/4mz9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4mz9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4mz9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SSB_ECOLI SSB_ECOLI]] This protein is essential for replication of the chromosomes and its single-stranded DNA phages. It is also involved in DNA recombination and repair.	+	[https://www.uniprot.org/uniprot/SSB_ECOLI SSB_ECOLI] This protein is essential for replication of the chromosomes and its single-stranded DNA phages. It is also involved in DNA recombination and repair.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~The single~~-stranded DNA (ssDNA) binding protein ~~from Escherichia coli~~ (~~EcoSSB~~) ~~plays~~ a ~~central role in DNA replication~~, ~~recombination~~ and ~~repair~~. The ~~tertiary structure~~ of ~~EcoSSB was determined at 2.2 A resolution. This is rather higher resolution than previously reported. Crystals were grown from~~ the ~~homogeneous intact protein~~ but ~~the EcoSSB tetramer in the crystals contains truncated subunits lacking a part~~ of the C-~~terminal~~. The structure ~~determined includes biologically important flexible loops~~ and C-~~terminal regions,~~ and ~~revealed~~ the ~~existence~~ of ~~concavities. These concavities include~~ the ~~residues important for~~ ssDNA ~~binding~~. ~~An ssDNA can be fitted on~~ the ~~concavities~~ and ~~further stabilized through interactions~~ with the ~~loops forming flexible lids. It seems likely to play a central role~~ in the ~~binding of ssDNA~~.	+	Single-stranded DNA (ssDNA) binding protein (SSB) is an essential protein to protect ssDNA and recruit specific ssDNA-processing proteins. Escherichia coli SSB forms a tetramer at neutral pH, comprising a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain) of approximately 64 amino acid residues. The C-terminal eight-residue segment of SSB (C-peptide) has been shown to interact with the OB-domain, but crystal structures failed to reveal any electron density of the C-peptide. Here we show that SSB forms a monomer at pH 3.4, which is suitable for studies by high-resolution nuclear magnetic resonance (NMR) spectroscopy. The OB-domain retains its 3D structure in the monomer, and the C-peptide is shown by nuclear Overhauser effects and lanthanide-induced pseudocontact shifts to bind to the OB-domain at a site that harbors ssDNA in the crystal structure of the SSB-ssDNA complex. 15N relaxation data demonstrate high flexibility of the polypeptide segment linking the C-peptide to the OB-domain and somewhat increased flexibility of the C-peptide compared with the OB-domain, suggesting that the C-peptide either retains high mobility in the bound state or is in a fast equilibrium with an unbound state.

-	~~Roles~~ of ~~functional loops and~~ the C-~~terminal segment~~ of a single-stranded DNA binding protein ~~elucidated~~ by ~~X-Ray structure analysis~~.,~~Matsumoto T~~, ~~Morimoto~~ Y, ~~Shibata N~~, ~~Kinebuchi T~~, ~~Shimamoto N~~, ~~Tsukihara~~ T, ~~Yasuoka N J Biochem~~. ~~2000 Feb;127(2):329-35~~. PMID:~~10731701~~<ref>PMID:~~10731701~~</ref>	+	Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy.,Shishmarev D, Wang Y, Mason CE, Su XC, Oakley AJ, Graham B, Huber T, Dixon NE, Otting G Nucleic Acids Res. 2013 Nov 27. PMID:24288378<ref>PMID:24288378</ref>

	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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Oakley, A J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Oakley AJ]]
-	~~[[Category: Dnag]]~~	+
-	~~[[Category: Exoi]]~~	+
-	~~[[Category: Holc]]~~	+
-	~~[[Category: Reco]]~~	+
-	~~[[Category: Recq]]~~	+
-	~~[[Category: Single strand dna-binding domain]]~~	+
-	~~[[Category: Ssb~~]]	+

OCA at 01:53, 5 August 2016

2016-08-05T01:53:03Z

←Older revision		Revision as of 01:53, 5 August 2016
Line 1:		Line 1:
		+
	==Revised structure of E. coli SSB==		==Revised structure of E. coli SSB==
	<StructureSection load='4mz9' size='340' side='right' caption='[[4mz9]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4mz9' size='340' side='right' caption='[[4mz9]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qvc\|1qvc]], [[1sru\|1sru]], [[1eyg\|1eyg]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qvc\|1qvc]], [[1sru\|1sru]], [[1eyg\|1eyg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4059, exrB, JW4020, lexC, ssb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4059, exrB, JW4020, lexC, ssb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [http://www.ebi.ac.uk/pdbsum/4mz9 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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [http://pdbe.org/4mz9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [http://www.ebi.ac.uk/pdbsum/4mz9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mz9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4mz9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:46, 24 December 2014

2014-12-24T21:46:34Z

←Older revision		Revision as of 21:46, 24 December 2014
Line 7:		Line 7:
	<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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [http://www.ebi.ac.uk/pdbsum/4mz9 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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [http://www.ebi.ac.uk/pdbsum/4mz9 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SSB_ECOLI SSB_ECOLI]] This protein is essential for replication of the chromosomes and its single-stranded DNA phages. It is also involved in DNA recombination and repair.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:21, 21 December 2014

2014-12-21T18:21:19Z

←Older revision		Revision as of 18:21, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4mz9\| PDB~~=4mz9 \| ~~SCENE~~= }}	+	==Revised structure of E. coli SSB==
-	===~~Revised~~ structure ~~of E~~. ~~coli SSB~~===	+	<StructureSection load='4mz9' size='340' side='right' caption='[[4mz9]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_10731701}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4mz9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MZ9 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1qvc\|1qvc]], [[1sru\|1sru]], [[1eyg\|1eyg]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b4059, exrB, JW4020, lexC, ssb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4mz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mz9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mz9 RCSB], [http://www.ebi.ac.uk/pdbsum/4mz9 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The single-stranded DNA (ssDNA) binding protein from Escherichia coli (EcoSSB) plays a central role in DNA replication, recombination and repair. The tertiary structure of EcoSSB was determined at 2.2 A resolution. This is rather higher resolution than previously reported. Crystals were grown from the homogeneous intact protein but the EcoSSB tetramer in the crystals contains truncated subunits lacking a part of the C-terminal. The structure determined includes biologically important flexible loops and C-terminal regions, and revealed the existence of concavities. These concavities include the residues important for ssDNA binding. An ssDNA can be fitted on the concavities and further stabilized through interactions with the loops forming flexible lids. It seems likely to play a central role in the binding of ssDNA.

-	~~==Function==~~	+	Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis.,Matsumoto T, Morimoto Y, Shibata N, Kinebuchi T, Shimamoto N, Tsukihara T, Yasuoka N J Biochem. 2000 Feb;127(2):329-35. PMID:10731701<ref>PMID:10731701</ref>
-	~~[[http://www.uniprot.org/uniprot/SSB_ECOLI SSB_ECOLI]] This protein is essential for replication~~ of ~~the chromosomes~~ and ~~its~~ single-stranded DNA ~~phages~~. ~~It is also involved in DNA recombination and repair~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4mz9]] is~~ a ~~4 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4MZ9 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:010731701</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
-	[[Category: Oakley, A J.]]	+	</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Oakley, A J]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Dnag]]		[[Category: Dnag]]

OCA at 10:17, 18 December 2013

2013-12-18T10:17:32Z

←Older revision		Revision as of 10:17, 18 December 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4mz9\| PDB=4mz9 \| SCENE= }}
		+	===Revised structure of E. coli SSB===
		+	{{ABSTRACT_PUBMED_10731701}}

-	~~The entry 4mz9~~ is ~~ON HOLD~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/SSB_ECOLI SSB_ECOLI]] This protein is essential for replication of the chromosomes and its single-stranded DNA phages. It is also involved in DNA recombination and repair.

-	~~Authors~~: ~~Oakley, A~~.J.	+	==About this Structure==
		+	[[4mz9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZ9 OCA].

-	~~Description~~: ~~Revised structure of E~~. ~~coli SSB~~	+	==Reference==
		+	<ref group="xtra">PMID:010731701</ref><references group="xtra"/><references/>
		+	[[Category: Oakley, A J.]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dnag]]
		+	[[Category: Exoi]]
		+	[[Category: Holc]]
		+	[[Category: Reco]]
		+	[[Category: Recq]]
		+	[[Category: Single strand dna-binding domain]]
		+	[[Category: Ssb]]

OCA: Protected "4mz9" [edit=sysop:move=sysop]

2013-10-10T05:51:27Z

Protected "4mz9" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:51, 10 October 2013

OCA: New page: '''Unreleased structure''' The entry 4mz9 is ON HOLD Authors: Oakley, A.J. Description: Revised structure of E. coli SSB

2013-10-10T05:51:26Z

New page: '''Unreleased structure''' The entry 4mz9 is ON HOLD Authors: Oakley, A.J. Description: Revised structure of E. coli SSB

New page

'''Unreleased structure'''

The entry 4mz9 is ON HOLD

Authors: Oakley, A.J.

Description: Revised structure of E. coli SSB