4xid - Revision history

OCA at 07:46, 27 September 2023

OCA — Wed, 27 Sep 2023 07:46:04 GMT

←Older revision		Revision as of 07:46, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xid]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XID FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xid]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XID FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.701Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [https://pdbe.org/4xid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [https://www.ebi.ac.uk/pdbsum/4xid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xid 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=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [https://pdbe.org/4xid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [https://www.ebi.ac.uk/pdbsum/4xid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xid ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:36, 26 April 2023

OCA — Wed, 26 Apr 2023 17:36:56 GMT

←Older revision		Revision as of 17:36, 26 April 2023
Line 1:		Line 1:

	==AntpHD with 15bp DNA duplex==		==AntpHD with 15bp DNA duplex==
-	<StructureSection load='4xid' size='340' side='right' caption='[[4xid]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='4xid' size='340' side='right'caption='[[4xid]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xid]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XID OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XID FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xid]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XID FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xic\|4xic]]</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=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [https://pdbe.org/4xid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [https://www.ebi.ac.uk/pdbsum/4xid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xid ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Antp, CG1028 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])~~</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=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [~~http~~://pdbe.org/4xid PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xid PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xid ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ANTP_DROME ANTP_DROME]] Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis.	+	[https://www.uniprot.org/uniprot/ANTP_DROME ANTP_DROME] Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
-	[[Category: ~~Iwahara, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~White, M A~~]]	+	[[Category: Unidentified]]
-	[[Category: ~~Zandarashvili, L~~]]	+	[[Category: Iwahara J]]
-	[[Category: ~~Dna-binding protein~~]]	+	[[Category: White MA]]
-	[[Category: ~~Homeodomain]]~~	+	[[Category: Zandarashvili L]]
-	~~[[Category: Transcription regulator-dna complex]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 09:34, 22 November 2017

OCA — Wed, 22 Nov 2017 09:34:50 GMT

←Older revision		Revision as of 09:34, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4xid' size='340' side='right' caption='[[4xid]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4xid' size='340' side='right' caption='[[4xid]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xid]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XID FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xid]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XID FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xic\|4xic]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xic\|4xic]]</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=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [http://pdbe.org/4xid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [http://www.ebi.ac.uk/pdbsum/4xid PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Antp, CG1028 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [http://pdbe.org/4xid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [http://www.ebi.ac.uk/pdbsum/4xid PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xid ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Iwahara, J]]		[[Category: Iwahara, J]]
	[[Category: White, M A]]		[[Category: White, M A]]

OCA at 18:55, 10 May 2016

OCA — Tue, 10 May 2016 18:55:33 GMT

←Older revision		Revision as of 18:55, 10 May 2016
Line 1:		Line 1:
		+
	==AntpHD with 15bp DNA duplex==		==AntpHD with 15bp DNA duplex==
	<StructureSection load='4xid' size='340' side='right' caption='[[4xid]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4xid' size='340' side='right' caption='[[4xid]], [[Resolution\|resolution]] 2.70Å' scene=''>

OCA at 04:36, 1 December 2015

OCA — Tue, 01 Dec 2015 04:36:38 GMT

←Older revision		Revision as of 04:36, 1 December 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==AntpHD with 15bp DNA duplex==
		+	<StructureSection load='4xid' size='340' side='right' caption='[[4xid]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xid]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XID FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xic\|4xic]]</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=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [http://pdbe.org/4xid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [http://www.ebi.ac.uk/pdbsum/4xid PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ANTP_DROME ANTP_DROME]] Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3(+) groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.

-	~~The entry 4xid is ON HOLD until Paper Publication~~	+	Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.,Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J Biophys J. 2015 Sep 1;109(5):1026-37. doi: 10.1016/j.bpj.2015.07.032. PMID:26331260<ref>PMID:26331260</ref>

-	~~Authors: White~~, M.A.~~, Zandarashvili, L., Iwahara, J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~AntpHD with 15bp DNA duplex~~	+	<div class="pdbe-citations 4xid" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Iwahara, J]]
		+	[[Category: White, M A]]
	[[Category: Zandarashvili, L]]		[[Category: Zandarashvili, L]]
-	[[Category: ~~White, M.A~~]]	+	[[Category: Dna-binding protein]]
-	[[Category: ~~Iwahara, J~~]]	+	[[Category: Homeodomain]]
		+	[[Category: Transcription regulator-dna complex]]
		+	[[Category: Transcription-dna complex]]

OCA at 09:50, 18 March 2015

OCA — Wed, 18 Mar 2015 09:50:32 GMT

←Older revision		Revision as of 09:50, 18 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: White, M.A., Zandarashvili, L., Iwahara, J.		Authors: White, M.A., Zandarashvili, L., Iwahara, J.

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

OCA — Wed, 14 Jan 2015 12:45:50 GMT

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

←Older revision

Revision as of 12:45, 14 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xid is ON HOLD Authors: White, M.A., Zandarashvili, L., Iwahara, J. Description: AntpHD with 15bp DNA duplex Category: Unreleased Structures [...

OCA — Wed, 14 Jan 2015 12:45:49 GMT

New page: '''Unreleased structure''' The entry 4xid is ON HOLD Authors: White, M.A., Zandarashvili, L., Iwahara, J. Description: AntpHD with 15bp DNA duplex Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 4xid is ON HOLD

Authors: White, M.A., Zandarashvili, L., Iwahara, J.

Description: AntpHD with 15bp DNA duplex
[[Category: Unreleased Structures]]
[[Category: Zandarashvili, L]]
[[Category: White, M.A]]
[[Category: Iwahara, J]]