5bpd - Revision history

OCA at 11:43, 9 May 2024

2024-05-09T11:43:33Z

←Older revision		Revision as of 11:43, 9 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BPD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BPD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [https://pdbe.org/5bpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [https://www.ebi.ac.uk/pdbsum/5bpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpd 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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [https://pdbe.org/5bpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [https://www.ebi.ac.uk/pdbsum/5bpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpd ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:02, 7 June 2023

2023-06-07T06:02:42Z

←Older revision		Revision as of 06:02, 7 June 2023
Line 3:		Line 3:
	<StructureSection load='5bpd' size='340' side='right'caption='[[5bpd]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5bpd' size='340' side='right'caption='[[5bpd]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43587 Atcc 43587~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BPD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BPD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trmBL2, PF0496 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])~~</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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [https://pdbe.org/5bpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [https://www.ebi.ac.uk/pdbsum/5bpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpd 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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [~~http~~://pdbe.org/5bpd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bpd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TMBL2_PYRFU TMBL2_PYRFU]] Binds to the maltodextrin transport gene cluster (mdxE operon) promoter and to some other TGM (Thermococcales-Glycolytic-Motif) sequences, but not exclusively.<ref>PMID:17587231</ref>	+	[https://www.uniprot.org/uniprot/TMBL2_PYRFU TMBL2_PYRFU] Binds to the maltodextrin transport gene cluster (mdxE operon) promoter and to some other TGM (Thermococcales-Glycolytic-Motif) sequences, but not exclusively.<ref>PMID:17587231</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43587]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ahmad, M U~~]]	+	[[Category: Pyrococcus furiosus]]
-	[[Category: ~~Diederichs, K~~]]	+	[[Category: Ahmad MU]]
-	[[Category: ~~Welte, W~~]]	+	[[Category: Diederichs K]]
-	[[Category: ~~Archaea]]~~	+	[[Category: Welte W]]
-	~~[[Category: Chromatin binding protein]]~~	+
-	~~[[Category: Dna binding protein~~]]	+

OCA at 06:18, 16 October 2019

2019-10-16T06:18:54Z

←Older revision		Revision as of 06:18, 16 October 2019
Line 1:		Line 1:
		+
	==Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.==		==Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.==
-	<StructureSection load='5bpd' size='340' side='right' caption='[[5bpd]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5bpd' size='340' side='right'caption='[[5bpd]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BPD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BPD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [http://pdbe.org/5bpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [http://www.ebi.ac.uk/pdbsum/5bpd PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trmBL2, PF0496 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [http://pdbe.org/5bpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [http://www.ebi.ac.uk/pdbsum/5bpd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bpd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43587]]
		+	[[Category: Large Structures]]
	[[Category: Ahmad, M U]]		[[Category: Ahmad, M U]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]

OCA at 07:43, 7 October 2015

2015-10-07T07:43:01Z

←Older revision		Revision as of 07:43, 7 October 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BPD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BPD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [http://www.ebi.ac.uk/pdbsum/5bpd 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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [http://pdbe.org/5bpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [http://www.ebi.ac.uk/pdbsum/5bpd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		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 5bpd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:27, 2 September 2015

2015-09-02T12:27:32Z

←Older revision		Revision as of 12:27, 2 September 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.==
		+	<StructureSection load='5bpd' size='340' side='right' caption='[[5bpd]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5bpd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BPD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></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=5bpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bpd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5bpd RCSB], [http://www.ebi.ac.uk/pdbsum/5bpd PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TMBL2_PYRFU TMBL2_PYRFU]] Binds to the maltodextrin transport gene cluster (mdxE operon) promoter and to some other TGM (Thermococcales-Glycolytic-Motif) sequences, but not exclusively.<ref>PMID:17587231</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of TrmBL2 from the archaeon P. furiosus shows an association of two pseudo-symmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix domains binding to successive major grooves of the DNA. However, in TrmBL2 the two dimers are arranged at a mutual displacement of approximately two base pairs so that they associate with the DNA along the double helical axis at an angle of approximately 80 degrees . While the deoxyribose phosphate groups of the dsDNA used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The helix-turn-helix domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent. This hitherto unseen mode of DNA binding by TrmBL2 seem to arise from non-optimal protein-DNA contacts made by its four helix-turn-helix domains resulting in a low-affinity, nonspecific binding to DNA.

-	~~The entry 5bpd is ON HOLD until Paper Publication~~	+	Structural insights into nonspecific binding of DNA by TrmBL2, an archaeal chromatin protein.,Ahmad MU, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W J Mol Biol. 2015 Aug 20. pii: S0022-2836(15)00458-1. doi:, 10.1016/j.jmb.2015.08.012. PMID:26299937<ref>PMID:26299937</ref>

-	~~Authors: Ahmad~~, M.U.~~, Diederichs, K~~.~~, Welte, W~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description:~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ahmad, M U]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]
	[[Category: Welte, W]]		[[Category: Welte, W]]
-	[[Category: ~~Ahmad, M.U~~]]	+	[[Category: Archaea]]
		+	[[Category: Chromatin binding protein]]
		+	[[Category: Dna binding protein]]

OCA at 13:19, 8 July 2015

2015-07-08T13:19:41Z

←Older revision		Revision as of 13:19, 8 July 2015
Line 5:		Line 5:
	Authors: Ahmad, M.U., Diederichs, K., Welte, W.		Authors: Ahmad, M.U., Diederichs, K., Welte, W.

-	Description: ~~Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Diederichs, K]]		[[Category: Diederichs, K]]
	[[Category: Welte, W]]		[[Category: Welte, W]]
	[[Category: Ahmad, M.U]]		[[Category: Ahmad, M.U]]

OCA at 12:51, 10 June 2015

2015-06-10T12:51:00Z

←Older revision		Revision as of 12:51, 10 June 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

-	Authors: Ahmad, M.U.	+	Authors: Ahmad, M.U., Diederichs, K., Welte, W.

-	Description: TrmBL2~~-TGM17 Complex~~	+	Description: Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Diederichs, K]]
		+	[[Category: Welte, W]]
	[[Category: Ahmad, M.U]]		[[Category: Ahmad, M.U]]

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

2015-06-03T11:45:46Z

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

←Older revision

Revision as of 11:45, 3 June 2015

OCA: New page: '''Unreleased structure''' The entry 5bpd is ON HOLD Authors: Ahmad, M.U. Description: TrmBL2-TGM17 Complex Category: Unreleased Structures Category: Ahmad, M.U

2015-06-03T11:45:44Z

New page: '''Unreleased structure''' The entry 5bpd is ON HOLD Authors: Ahmad, M.U. Description: TrmBL2-TGM17 Complex Category: Unreleased Structures Category: Ahmad, M.U

New page

'''Unreleased structure'''

The entry 5bpd is ON HOLD

Authors: Ahmad, M.U.

Description: TrmBL2-TGM17 Complex
[[Category: Unreleased Structures]]
[[Category: Ahmad, M.U]]