4omz - Revision history

OCA at 12:41, 1 March 2024

OCA — Fri, 01 Mar 2024 12:41:00 GMT

←Older revision		Revision as of 12:41, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4omz]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_fredii Sinorhizobium fredii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OMZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4omz]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_fredii Sinorhizobium fredii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OMZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.64Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [https://pdbe.org/4omz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [https://www.ebi.ac.uk/pdbsum/4omz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4omz 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=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [https://pdbe.org/4omz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [https://www.ebi.ac.uk/pdbsum/4omz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4omz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q83TD2_RHIFR Q83TD2_RHIFR]		[https://www.uniprot.org/uniprot/Q83TD2_RHIFR Q83TD2_RHIFR]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory protein. Here, we present the X-ray crystal structures of NolR in the unliganded form and complexed with two different 22-base pair (bp) double-stranded operator sequences (oligos AT and AA). Structural and biochemical analysis of NolR reveals protein-DNA interactions with an asymmetric operator site and defines a mechanism for conformational switching of a key residue (Gln56) to accommodate variation in target DNA sequences from diverse rhizobial genes for nodulation and symbiosis. This conformational switching alters the energetic contributions to DNA binding without changes in affinity for the target sequence. Two possible models for the role of NolR in the regulation of different nodulation and symbiosis genes are proposed. To our knowledge, these studies provide the first structural insight on the regulation of genes involved in the agriculturally and ecologically important symbiosis of microbes and plants that leads to nodule formation and nitrogen fixation.
-
-	Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.,Lee SG, Krishnan HB, Jez JM Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6509-14. doi:, 10.1073/pnas.1402243111. Epub 2014 Apr 14. PMID:24733893<ref>PMID:24733893</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4omz" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:34, 25 January 2023

OCA — Wed, 25 Jan 2023 07:34:10 GMT

←Older revision		Revision as of 07:34, 25 January 2023
Line 1:		Line 1:

	==Crystal Structure of NolR from Sinorhizobium fredii==		==Crystal Structure of NolR from Sinorhizobium fredii==
-	<StructureSection load='4omz' size='340' side='right' caption='[[4omz]], [[Resolution\|resolution]] 2.64Å' scene=''>	+	<StructureSection load='4omz' size='340' side='right'caption='[[4omz]], [[Resolution\|resolution]] 2.64Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4omz]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_35423 Atcc 35423~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4omz]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_fredii Sinorhizobium fredii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OMZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nolR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=380 ATCC 35423])~~</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=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [https://pdbe.org/4omz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [https://www.ebi.ac.uk/pdbsum/4omz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4omz 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=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [~~http~~://pdbe.org/4omz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4omz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4omz ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q83TD2_RHIFR Q83TD2_RHIFR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 35423~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Jez, J M~~]]	+	[[Category: Sinorhizobium fredii]]
-	[[Category: ~~Krishnan, H B~~]]	+	[[Category: Jez JM]]
-	[[Category: ~~Lee, S G~~]]	+	[[Category: Krishnan HB]]
-	[[Category: ~~Helix-turn-helix]]~~	+	[[Category: Lee SG]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulator~~]]	+

OCA at 12:14, 11 August 2016

OCA — Thu, 11 Aug 2016 12:14:36 GMT

←Older revision		Revision as of 12:14, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of NolR from Sinorhizobium fredii==		==Crystal Structure of NolR from Sinorhizobium fredii==
	<StructureSection load='4omz' size='340' side='right' caption='[[4omz]], [[Resolution\|resolution]] 2.64Å' scene=''>		<StructureSection load='4omz' size='340' side='right' caption='[[4omz]], [[Resolution\|resolution]] 2.64Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nolR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=380 ATCC 35423])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nolR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=380 ATCC 35423])</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=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [http://www.ebi.ac.uk/pdbsum/4omz 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=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [http://pdbe.org/4omz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [http://www.ebi.ac.uk/pdbsum/4omz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4omz 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 4omz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:45, 5 January 2015

OCA — Mon, 05 Jan 2015 09:45:18 GMT

←Older revision		Revision as of 09:45, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4omz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35423 Atcc 35423]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OMZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4omz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35423 Atcc 35423]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OMZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nolR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=380 ATCC 35423])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nolR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=380 ATCC 35423])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [http://www.ebi.ac.uk/pdbsum/4omz 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=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [http://www.ebi.ac.uk/pdbsum/4omz PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 13:
	Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.,Lee SG, Krishnan HB, Jez JM Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6509-14. doi:, 10.1073/pnas.1402243111. Epub 2014 Apr 14. PMID:24733893<ref>PMID:24733893</ref>		Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.,Lee SG, Krishnan HB, Jez JM Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6509-14. doi:, 10.1073/pnas.1402243111. Epub 2014 Apr 14. PMID:24733893<ref>PMID:24733893</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 35423]]		[[Category: Atcc 35423]]
-	[[Category: Jez, J M.]]	+	[[Category: Jez, J M]]
-	[[Category: Krishnan, H B.]]	+	[[Category: Krishnan, H B]]
-	[[Category: Lee, S G.]]	+	[[Category: Lee, S G]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulator]]		[[Category: Transcription regulator]]

OCA at 04:42, 4 June 2014

OCA — Wed, 04 Jun 2014 04:42:05 GMT

←Older revision		Revision as of 04:42, 4 June 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4omz\| PDB=4omz \| SCENE= }}~~	+	==Crystal Structure of NolR from Sinorhizobium fredii==
-	===Crystal Structure of NolR from Sinorhizobium fredii===	+	<StructureSection load='4omz' size='340' side='right' caption='[[4omz]], [[Resolution\|resolution]] 2.64Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4omz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35423 Atcc 35423]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OMZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nolR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=380 ATCC 35423])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4omz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4omz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4omz RCSB], [http://www.ebi.ac.uk/pdbsum/4omz PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory protein. Here, we present the X-ray crystal structures of NolR in the unliganded form and complexed with two different 22-base pair (bp) double-stranded operator sequences (oligos AT and AA). Structural and biochemical analysis of NolR reveals protein-DNA interactions with an asymmetric operator site and defines a mechanism for conformational switching of a key residue (Gln56) to accommodate variation in target DNA sequences from diverse rhizobial genes for nodulation and symbiosis. This conformational switching alters the energetic contributions to DNA binding without changes in affinity for the target sequence. Two possible models for the role of NolR in the regulation of different nodulation and symbiosis genes are proposed. To our knowledge, these studies provide the first structural insight on the regulation of genes involved in the agriculturally and ecologically important symbiosis of microbes and plants that leads to nodule formation and nitrogen fixation.

-	~~==About this Structure==~~	+	Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR.,Lee SG, Krishnan HB, Jez JM Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6509-14. doi:, 10.1073/pnas.1402243111. Epub 2014 Apr 14. PMID:24733893<ref>PMID:24733893</ref>
-	~~[[4omz]] is a 8 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin~~/~~ocashort?id~~=~~4OMZ OCA~~].	+
		+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 35423]]
	[[Category: Jez, J M.]]		[[Category: Jez, J M.]]
	[[Category: Krishnan, H B.]]		[[Category: Krishnan, H B.]]

OCA at 10:08, 16 April 2014

OCA — Wed, 16 Apr 2014 10:08:50 GMT

←Older revision		Revision as of 10:08, 16 April 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4omz\| PDB=4omz \| SCENE= }}
		+	===Crystal Structure of NolR from Sinorhizobium fredii===

-	~~The entry~~ 4omz is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4omz]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OMZ OCA].
-	~~Authors~~: ~~Lee, S~~.G., Krishnan, H.B., ~~Jez, J.M~~.	+	[[Category: Jez, J M.]]
-		+	[[Category: Krishnan, H B.]]
-	~~Description~~: ~~Crystal Structure of NolR from Sinorhizobium fredii~~	+	[[Category: Lee, S G.]]
		+	[[Category: Helix-turn-helix]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulator]]

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

OCA — Wed, 05 Feb 2014 10:33:52 GMT

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

←Older revision

Revision as of 10:33, 5 February 2014

OCA: New page: '''Unreleased structure''' The entry 4omz is ON HOLD Authors: Lee, S.G., Krishnan, H.B., Jez, J.M. Description: Crystal Structure of NolR from Sinorhizobium fredii

OCA — Wed, 05 Feb 2014 10:33:51 GMT

New page: '''Unreleased structure''' The entry 4omz is ON HOLD Authors: Lee, S.G., Krishnan, H.B., Jez, J.M. Description: Crystal Structure of NolR from Sinorhizobium fredii

New page

'''Unreleased structure'''

The entry 4omz is ON HOLD

Authors: Lee, S.G., Krishnan, H.B., Jez, J.M.

Description: Crystal Structure of NolR from Sinorhizobium fredii