3w1o - Revision history

OCA at 08:43, 20 March 2024

OCA — Wed, 20 Mar 2024 08:43:30 GMT

←Older revision		Revision as of 08:43, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3w1o' size='340' side='right'caption='[[3w1o]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3w1o' size='340' side='right'caption='[[3w1o]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w1o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Neimb Neimb~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w1o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_MC58 Neisseria meningitidis MC58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W1O FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.85Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~NMB2123 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 NEIMB])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=3w1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1o OCA], [https://pdbe.org/3w1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w1o RCSB], [https://www.ebi.ac.uk/pdbsum/3w1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w1o 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=3w1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1o OCA], [https://pdbe.org/3w1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w1o RCSB], [https://www.ebi.ac.uk/pdbsum/3w1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w1o ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9JXC6_NEIMB Q9JXC6_NEIMB]
-	DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.	+
-		+
-	~~Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein.,Wang HC, Wu ML, Ko TP, Wang AH Nucleic Acids Res. 2013 Mar 26. PMID~~:~~23531546<ref>PMID:23531546<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3w1o" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Neimb~~]]	+	[[Category: Neisseria meningitidis MC58]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Ko TP]]
-	[[Category: Wang~~, A H.J~~]]	+	[[Category: Wang AHJ]]
-	[[Category: Wang~~, H C~~]]	+	[[Category: Wang HC]]
-	[[Category: Wu~~, M L]]~~	+	[[Category: Wu ML]]
-	~~[[Category: Dna mimic]]~~	+
-	~~[[Category: Hu protein]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 05:18, 3 August 2022

OCA — Wed, 03 Aug 2022 05:18:26 GMT

←Older revision		Revision as of 05:18, 3 August 2022
Line 1:		Line 1:

	==Neisseria DNA mimic protein DMP12==		==Neisseria DNA mimic protein DMP12==
-	<StructureSection load='3w1o' size='340' side='right' caption='[[3w1o]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3w1o' size='340' side='right'caption='[[3w1o]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w1o]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Neimb Neimb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3W1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w1o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neimb Neimb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W1O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NMB2123 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 NEIMB])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NMB2123 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 NEIMB])</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=3w1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1o OCA], [~~http~~://pdbe.org/3w1o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3w1o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3w1o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3w1o 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=3w1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1o OCA], [https://pdbe.org/3w1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w1o RCSB], [https://www.ebi.ac.uk/pdbsum/3w1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w1o ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Neimb]]		[[Category: Neimb]]
	[[Category: Ko, T P]]		[[Category: Ko, T P]]

OCA at 16:53, 11 August 2016

OCA — Thu, 11 Aug 2016 16:53:31 GMT

←Older revision		Revision as of 16:53, 11 August 2016
Line 1:		Line 1:
		+
	==Neisseria DNA mimic protein DMP12==		==Neisseria DNA mimic protein DMP12==
	<StructureSection load='3w1o' size='340' side='right' caption='[[3w1o]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3w1o' size='340' side='right' caption='[[3w1o]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Neisseria_meningitidis_mc58 Neisseria meningitidis mc58~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neimb Neimb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W1O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NMB2123 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 ~~Neisseria meningitidis MC58~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NMB2123 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 NEIMB])</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=3w1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w1o RCSB], [http://www.ebi.ac.uk/pdbsum/3w1o 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=3w1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1o OCA], [http://pdbe.org/3w1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w1o RCSB], [http://www.ebi.ac.uk/pdbsum/3w1o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w1o 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 3w1o" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Neisseria meningitidis mc58~~]]	+	[[Category: Neimb]]
	[[Category: Ko, T P]]		[[Category: Ko, T P]]
	[[Category: Wang, A H.J]]		[[Category: Wang, A H.J]]

OCA at 10:19, 4 January 2015

OCA — Sun, 04 Jan 2015 10:19:59 GMT

←Older revision		Revision as of 10:19, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3w1o~~\| ~~PDB~~=3w1o \| ~~SCENE~~= }}	+	==Neisseria DNA mimic protein DMP12==
-	===Neisseria ~~DNA mimic protein DMP12~~===	+	<StructureSection load='3w1o' size='340' side='right' caption='[[3w1o]], [[Resolution\|resolution]] 1.85Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23531546}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3w1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neisseria_meningitidis_mc58 Neisseria meningitidis mc58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W1O FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NMB2123 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 Neisseria meningitidis MC58])</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=3w1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w1o RCSB], [http://www.ebi.ac.uk/pdbsum/3w1o PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

-	~~==About this Structure==~~	+	Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein.,Wang HC, Wu ML, Ko TP, Wang AH Nucleic Acids Res. 2013 Mar 26. PMID:23531546<ref>PMID:23531546</ref>
-	~~[[3w1o]]~~ is a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Neisseria_meningitidis_mc58 Neisseria meningitidis mc58]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023531546</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Neisseria meningitidis mc58]]		[[Category: Neisseria meningitidis mc58]]
-	[[Category: Ko, T P.]]	+	[[Category: Ko, T P]]
-	[[Category: Wang, A H.J.]]	+	[[Category: Wang, A H.J]]
-	[[Category: Wang, H C.]]	+	[[Category: Wang, H C]]
-	[[Category: Wu, M L.]]	+	[[Category: Wu, M L]]
	[[Category: Dna mimic]]		[[Category: Dna mimic]]
	[[Category: Hu protein]]		[[Category: Hu protein]]
	[[Category: Protein binding]]		[[Category: Protein binding]]

OCA at 18:21, 19 June 2013

OCA — Wed, 19 Jun 2013 18:21:17 GMT

←Older revision		Revision as of 18:21, 19 June 2013
Line 5:		Line 5:
	==About this Structure==		==About this Structure==
	[[3w1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neisseria_meningitidis_mc58 Neisseria meningitidis mc58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA].		[[3w1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neisseria_meningitidis_mc58 Neisseria meningitidis mc58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023531546</ref><references group="xtra"/><references/>
	[[Category: Neisseria meningitidis mc58]]		[[Category: Neisseria meningitidis mc58]]
	[[Category: Ko, T P.]]		[[Category: Ko, T P.]]

OCA at 22:38, 10 April 2013

OCA — Wed, 10 Apr 2013 22:38:09 GMT

←Older revision		Revision as of 22:38, 10 April 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3w1o\| PDB=3w1o \| SCENE= }}
		+	===Neisseria DNA mimic protein DMP12===
		+	{{ABSTRACT_PUBMED_23531546}}

-	~~The entry~~ 3w1o is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3w1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Neisseria_meningitidis_mc58 Neisseria meningitidis mc58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W1O OCA].
-	~~Authors~~: ~~Wang, H~~.C.~~, Ko, T~~.P.~~, Wu, M~~.L., Wang, A.H.J.	+	[[Category: Neisseria meningitidis mc58]]
-		+	[[Category: Ko, T P.]]
-	~~Description~~: ~~Neisseria DNA~~ mimic protein ~~DMP12~~	+	[[Category: Wang, A H.J.]]
		+	[[Category: Wang, H C.]]
		+	[[Category: Wu, M L.]]
		+	[[Category: Dna mimic]]
		+	[[Category: Hu protein]]
		+	[[Category: Protein binding]]

OCA at 10:17, 5 December 2012

OCA — Wed, 05 Dec 2012 10:17:19 GMT

←Older revision		Revision as of 10:17, 5 December 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3w1o is ON HOLD	+	The entry 3w1o is ON HOLD until Paper Publication

-	Authors: ~~Hao-Ching~~ Wang, ~~Tzu-Ping~~ Ko, ~~Mao-Lun~~ Wu, ~~Andrew~~ H.-J. ~~Wang~~	+	Authors: Wang, H.C., Ko, T.P., Wu, M.L., Wang, A.H.J.

	Description: Neisseria DNA mimic protein DMP12		Description: Neisseria DNA mimic protein DMP12

OCA: Protected "3w1o" [edit=sysop:move=sysop]

OCA — Wed, 28 Nov 2012 13:50:49 GMT

Protected "3w1o" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:50, 28 November 2012

OCA: New page: '''Unreleased structure''' The entry 3w1o is ON HOLD Authors: Hao-Ching Wang, Tzu-Ping Ko, Mao-Lun Wu, Andrew H.-J. Wang Description: Neisseria DNA mimic protein DMP12

OCA — Wed, 28 Nov 2012 13:50:47 GMT

New page: '''Unreleased structure''' The entry 3w1o is ON HOLD Authors: Hao-Ching Wang, Tzu-Ping Ko, Mao-Lun Wu, Andrew H.-J. Wang Description: Neisseria DNA mimic protein DMP12

New page

'''Unreleased structure'''

The entry 3w1o is ON HOLD

Authors: Hao-Ching Wang, Tzu-Ping Ko, Mao-Lun Wu, Andrew H.-J. Wang

Description: Neisseria DNA mimic protein DMP12