4qju - Revision history

OCA at 15:07, 8 November 2023

OCA — Wed, 08 Nov 2023 15:07:06 GMT

←Older revision		Revision as of 15:07, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QJU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QJU 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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [https://pdbe.org/4qju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [https://www.ebi.ac.uk/pdbsum/4qju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qju 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]] 2.16Å</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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [https://pdbe.org/4qju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [https://www.ebi.ac.uk/pdbsum/4qju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qju ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 11:32, 15 February 2023

OCA — Wed, 15 Feb 2023 11:32:51 GMT

←Older revision		Revision as of 11:32, 15 February 2023
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	<StructureSection load='4qju' size='340' side='right'caption='[[4qju]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='4qju' size='340' side='right'caption='[[4qju]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staam Staam~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus aureus subsp. aureus Mu50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QJU FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qjn\|4qjn]]</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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [https://pdbe.org/4qju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [https://www.ebi.ac.uk/pdbsum/4qju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qju ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hup ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158878 STAAM])</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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [~~http~~://pdbe.org/4qju PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qju PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qju ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DBH_STAAM DBH_STAAM]] Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions.	+	[https://www.uniprot.org/uniprot/DBH_STAAM DBH_STAAM] Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Staam~~]]	+	[[Category: Staphylococcus aureus subsp. aureus Mu50]]
-	[[Category: Im, H]]	+	[[Category: Im H]]
-	[[Category: Kim, D H]]	+	[[Category: Kim D-H]]
-	[[Category: Lee, B J]]	+	[[Category: Lee B-J]]
-	[[Category: Yoon, H J]]	+	[[Category: Yoon H-J]]
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna condensation~~]]	+

OCA at 09:37, 24 April 2019

OCA — Wed, 24 Apr 2019 09:37:39 GMT

←Older revision		Revision as of 09:37, 24 April 2019
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	==Crystal structure of DNA-bound nucleoid associated protein, SAV1473==		==Crystal structure of DNA-bound nucleoid associated protein, SAV1473==
-	<StructureSection load='4qju' size='340' side='right' caption='[[4qju]], [[Resolution\|resolution]] 2.16Å' scene=''>	+	<StructureSection load='4qju' size='340' side='right'caption='[[4qju]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staam Staam]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QJU FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qjn\|4qjn]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qjn\|4qjn]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hup ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158878 STAAM])</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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [http://pdbe.org/4qju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [http://www.ebi.ac.uk/pdbsum/4qju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qju ProSAT]</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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [http://pdbe.org/4qju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [http://www.ebi.ac.uk/pdbsum/4qju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qju ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Staam]]
	[[Category: Im, H]]		[[Category: Im, H]]
	[[Category: Kim, D H]]		[[Category: Kim, D H]]

OCA at 22:26, 4 August 2016

OCA — Thu, 04 Aug 2016 22:26:10 GMT

←Older revision		Revision as of 22:26, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of DNA-bound nucleoid associated protein, SAV1473==		==Crystal structure of DNA-bound nucleoid associated protein, SAV1473==
	<StructureSection load='4qju' size='340' side='right' caption='[[4qju]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='4qju' size='340' side='right' caption='[[4qju]], [[Resolution\|resolution]] 2.16Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QJU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QJU FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qjn\|4qjn]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qjn\|4qjn]]</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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [http://www.ebi.ac.uk/pdbsum/4qju 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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [http://pdbe.org/4qju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [http://www.ebi.ac.uk/pdbsum/4qju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qju ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	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 4qju" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:13, 24 December 2014

OCA — Wed, 24 Dec 2014 20:13:37 GMT

←Older revision		Revision as of 20:13, 24 December 2014
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	<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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [http://www.ebi.ac.uk/pdbsum/4qju 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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [http://www.ebi.ac.uk/pdbsum/4qju PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DBH_STAAM DBH_STAAM]] Histone-like DNA-binding protein which is capable of wrapping DNA to stabilize it, and thus to prevent its denaturation under extreme environmental conditions.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 12:43, 17 December 2014

OCA — Wed, 17 Dec 2014 12:43:50 GMT

←Older revision		Revision as of 12:43, 17 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of DNA-bound nucleoid associated protein, SAV1473==
		+	<StructureSection load='4qju' size='340' side='right' caption='[[4qju]], [[Resolution\|resolution]] 2.16Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4qju]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QJU FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qjn\|4qjn]]</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=4qju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qju OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qju RCSB], [http://www.ebi.ac.uk/pdbsum/4qju PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	HU, one of the major nucleoid-associated proteins, interacts with the minor groove of DNA in a nonspecific manner to induce DNA bending or to stabilize bent DNA. In this study, crystal structures are reported for both free HU from Staphylococcus aureus Mu50 (SHU) and SHU bound to 21-mer dsDNA. The structures, in combination with electrophoretic mobility shift assays (EMSAs), isothermal titration calorimetry (ITC) measurements and molecular-dynamics (MD) simulations, elucidate the overall and residue-specific changes in SHU upon recognizing and binding to DNA. Firstly, structural comparison showed the flexible nature of the beta-sheets of the DNA-binding domain and that the beta-arms bend inwards upon complex formation, whereas the other portions are nearly unaltered. Secondly, it was found that the disruption and formation of salt bridges accompanies DNA binding. Thirdly, residue-specific free-energy analyses using the MM-PBSA method with MD simulation data suggested that the successive basic residues in the beta-arms play a central role in recognizing and binding to DNA, which was confirmed by the EMSA and ITC analyses. Moreover, residue Arg55 resides in the hinge region of the flexible beta-arms, exhibiting a remarkable role in their flexible nature. Fourthly, EMSAs with various DNAs revealed that SHU prefers deformable DNA. Taken together, these data suggest residue-specific roles in local shape and base readouts, which are primarily mediated by the flexible beta-arms consisting of residues 50-80.

-	~~The entry 4qju is ON HOLD until Paper Publication~~	+	beta-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism.,Kim do H, Im H, Jee JG, Jang SB, Yoon HJ, Kwon AR, Kang SM, Lee BJ Acta Crystallogr D Biol Crystallogr. 2014 Dec 1;70(Pt 12):3273-89. doi:, 10.1107/S1399004714023931. Epub 2014 Nov 28. PMID:25478845<ref>PMID:25478845</ref>

-	~~Authors: Lee~~, B.-J., Kim, D.-H~~., Im, H.~~, Yoon, H.-J.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of DNA-bound nucleoid associated~~ protein	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Im, H]]
		+	[[Category: Kim, D H]]
		+	[[Category: Lee, B J]]
		+	[[Category: Yoon, H J]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna condensation]]

OCA at 05:55, 25 June 2014

OCA — Wed, 25 Jun 2014 05:55:21 GMT

←Older revision		Revision as of 05:55, 25 June 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Lee, B-.J., Kim, D-.H., Im, H., Yoon, H-.J.	+	Authors: Lee, B.-J., Kim, D.-H., Im, H., Yoon, H.-J.

	Description: Crystal structure of DNA-bound nucleoid associated protein		Description: Crystal structure of DNA-bound nucleoid associated protein

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

OCA — Wed, 11 Jun 2014 08:09:20 GMT

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

←Older revision

Revision as of 08:09, 11 June 2014

OCA: New page: '''Unreleased structure''' The entry 4qju is ON HOLD Authors: Lee, B-.J., Kim, D-.H., Im, H., Yoon, H-.J. Description: Crystal structure of DNA-bound nucleoid associated protein

OCA — Wed, 11 Jun 2014 08:09:19 GMT

New page: '''Unreleased structure''' The entry 4qju is ON HOLD Authors: Lee, B-.J., Kim, D-.H., Im, H., Yoon, H-.J. Description: Crystal structure of DNA-bound nucleoid associated protein

New page

'''Unreleased structure'''

The entry 4qju is ON HOLD

Authors: Lee, B-.J., Kim, D-.H., Im, H., Yoon, H-.J.

Description: Crystal structure of DNA-bound nucleoid associated protein