1d06 - Revision history

OCA at 06:47, 7 February 2024

OCA — Wed, 07 Feb 2024 06:47:15 GMT

←Older revision		Revision as of 06:47, 7 February 2024
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	<StructureSection load='1d06' size='340' side='right'caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='1d06' size='340' side='right'caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_9930 Atcc 9930~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D06 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D06 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [https://pdbe.org/1d06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [https://www.ebi.ac.uk/pdbsum/1d06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d06 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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [https://pdbe.org/1d06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [https://www.ebi.ac.uk/pdbsum/1d06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d06 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FIXL_RHIME FIXL_RHIME]] Putative oxygen sensor; modulates the activity of FixJ, a transcriptional activator of nitrogen fixation fixK gene. FixL probably acts as a kinase that phosphorylates FixJ.	+	[https://www.uniprot.org/uniprot/FIXL_RHIME FIXL_RHIME] Putative oxygen sensor; modulates the activity of FixJ, a transcriptional activator of nitrogen fixation fixK gene. FixL probably acts as a kinase that phosphorylates FixJ.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d06 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d06 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	FixL of Rhizobium meliloti (RmFixL) is a sensor histidine kinase of the two-component system, which regulates the expression of the genes related to nitrogen fixation in the root nodule in response to the O(2) levels. The crystal structure of the sensor domain of FixL (RmFixLH), which contains a heme (Fe-porphyrin) as a sensing site, was determined at 1.4 A resolution. Based on the structural and spectroscopic analyses, we propose the O(2) sensing mechanism that differs from the case proposed in BjFixLH as follows; conformational changes in the F/G loop, which are induced by steric repulsion between the bent-bound O(2) and the Ile209 side-chain, would be transmitted to the histidine kinase domain. Interaction between the iron-bound O(2) and Ile209 was also observed in the resonance Raman spectra of RmFixLH as evidenced by the fact that the Fe-O(2) and Fe-CN stretching frequencies were shifted from 575 to 570 cm(-1) (Fe-O(2)), and 504 to 499 cm(-1), respectively, as the result of the replacement of Ile209 with an Ala residue. In the I209A mutant of RmFixL, the O(2) sensing activity was destroyed, thus confirming our proposed mechanism.
-
-	Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies.,Miyatake H, Mukai M, Park SY, Adachi S, Tamura K, Nakamura H, Nakamura K, Tsuchiya T, Iizuka T, Shiro Y J Mol Biol. 2000 Aug 11;301(2):415-31. PMID:10926518<ref>PMID:10926518</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1d06" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 9930]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adachi, S]]	+	[[Category: Sinorhizobium meliloti]]
-	[[Category: Iizuka, T]]	+	[[Category: Adachi S]]
-	[[Category: Miyatake, H]]	+	[[Category: Iizuka T]]
-	[[Category: Mukai, M]]	+	[[Category: Miyatake H]]
-	[[Category: Nakamura, H]]	+	[[Category: Mukai M]]
-	[[Category: Nakamura, K]]	+	[[Category: Nakamura H]]
-	[[Category: Park, S Y]]	+	[[Category: Nakamura K]]
-	[[Category: Shiro, Y]]	+	[[Category: Park S-Y]]
-	[[Category: Tamura, K]]	+	[[Category: Shiro Y]]
-	[[Category: Tsuchiya, T]]	+	[[Category: Tamura K]]
-	~~[[Category: High-resolution]]~~	+	[[Category: Tsuchiya T]]
-	~~[[Category: Histidine kinase]]~~	+
-	~~[[Category: Oxygen sensor]]~~	+
-	~~[[Category: Pa]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Two-component system~~]]	+

OCA at 06:29, 11 August 2021

OCA — Wed, 11 Aug 2021 06:29:14 GMT

←Older revision		Revision as of 06:29, 11 August 2021
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	<StructureSection load='1d06' size='340' side='right'caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='1d06' size='340' side='right'caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1D06 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D06 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [~~http~~://pdbe.org/1d06 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1d06 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1d06 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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [https://pdbe.org/1d06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [https://www.ebi.ac.uk/pdbsum/1d06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d06 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FIXL_RHIME FIXL_RHIME]] Putative oxygen sensor; modulates the activity of FixJ, a transcriptional activator of nitrogen fixation fixK gene. FixL probably acts as a kinase that phosphorylates FixJ.	+	[[https://www.uniprot.org/uniprot/FIXL_RHIME FIXL_RHIME]] Putative oxygen sensor; modulates the activity of FixJ, a transcriptional activator of nitrogen fixation fixK gene. FixL probably acts as a kinase that phosphorylates FixJ.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:46, 6 November 2019

OCA — Wed, 06 Nov 2019 09:46:38 GMT

←Older revision		Revision as of 09:46, 6 November 2019
Line 1:		Line 1:

	==STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION==		==STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION==
-	<StructureSection load='1d06' size='340' side='right' caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='1d06' size='340' side='right'caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 9930]]		[[Category: Atcc 9930]]
		+	[[Category: Large Structures]]
	[[Category: Adachi, S]]		[[Category: Adachi, S]]
	[[Category: Iizuka, T]]		[[Category: Iizuka, T]]

OCA at 08:37, 6 December 2017

OCA — Wed, 06 Dec 2017 08:37:22 GMT

←Older revision		Revision as of 08:37, 6 December 2017
Line 1:		Line 1:
		+
	==STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION==		==STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION==
	<StructureSection load='1d06' size='340' side='right' caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='1d06' size='340' side='right' caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://pdbe.org/1d06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://pdbe.org/1d06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d06 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/1d06_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/1d06_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 14:13, 9 February 2016

OCA — Tue, 09 Feb 2016 14:13:06 GMT

←Older revision		Revision as of 14:13, 9 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d06 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:01, 10 September 2015

OCA — Thu, 10 Sep 2015 23:01:23 GMT

←Older revision		Revision as of 23:01, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1d06' size='340' side='right' caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='1d06' size='340' side='right' caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sinorhizobium_meliloti Sinorhizobium meliloti~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_9930 Atcc 9930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://pdbe.org/1d06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1d06" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sinorhizobium meliloti~~]]	+	[[Category: Atcc 9930]]
	[[Category: Adachi, S]]		[[Category: Adachi, S]]
	[[Category: Iizuka, T]]		[[Category: Iizuka, T]]

OCA at 07:19, 25 December 2014

OCA — Thu, 25 Dec 2014 07:19:02 GMT

←Older revision		Revision as of 07:19, 25 December 2014
Line 6:		Line 6:
	<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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FIXL_RHIME FIXL_RHIME]] Putative oxygen sensor; modulates the activity of FixJ, a transcriptional activator of nitrogen fixation fixK gene. FixL probably acts as a kinase that phosphorylates FixJ.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:06, 22 December 2014

OCA — Mon, 22 Dec 2014 19:06:26 GMT

←Older revision		Revision as of 19:06, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
-	[[Category: Adachi, S.]]	+	[[Category: Adachi, S]]
-	[[Category: Iizuka, T.]]	+	[[Category: Iizuka, T]]
-	[[Category: Miyatake, H.]]	+	[[Category: Miyatake, H]]
-	[[Category: Mukai, M.]]	+	[[Category: Mukai, M]]
-	[[Category: Nakamura, H.]]	+	[[Category: Nakamura, H]]
-	[[Category: Nakamura, K.]]	+	[[Category: Nakamura, K]]
-	[[Category: Park, S Y.]]	+	[[Category: Park, S Y]]
-	[[Category: Shiro, Y.]]	+	[[Category: Shiro, Y]]
-	[[Category: Tamura, K.]]	+	[[Category: Tamura, K]]
-	[[Category: Tsuchiya, T.]]	+	[[Category: Tsuchiya, T]]
	[[Category: High-resolution]]		[[Category: High-resolution]]
	[[Category: Histidine kinase]]		[[Category: Histidine kinase]]

OCA at 09:27, 27 August 2014

OCA — Wed, 27 Aug 2014 09:27:23 GMT

←Older revision		Revision as of 09:27, 27 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1d06.~~png\|left~~\|200px]]	+	==STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION==
		+	<StructureSection load='1d06' size='340' side='right' caption='[[1d06]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1d06]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D06 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<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=1d06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d06 RCSB], [http://www.ebi.ac.uk/pdbsum/1d06 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d0/1d06_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	FixL of Rhizobium meliloti (RmFixL) is a sensor histidine kinase of the two-component system, which regulates the expression of the genes related to nitrogen fixation in the root nodule in response to the O(2) levels. The crystal structure of the sensor domain of FixL (RmFixLH), which contains a heme (Fe-porphyrin) as a sensing site, was determined at 1.4 A resolution. Based on the structural and spectroscopic analyses, we propose the O(2) sensing mechanism that differs from the case proposed in BjFixLH as follows; conformational changes in the F/G loop, which are induced by steric repulsion between the bent-bound O(2) and the Ile209 side-chain, would be transmitted to the histidine kinase domain. Interaction between the iron-bound O(2) and Ile209 was also observed in the resonance Raman spectra of RmFixLH as evidenced by the fact that the Fe-O(2) and Fe-CN stretching frequencies were shifted from 575 to 570 cm(-1) (Fe-O(2)), and 504 to 499 cm(-1), respectively, as the result of the replacement of Ile209 with an Ala residue. In the I209A mutant of RmFixL, the O(2) sensing activity was destroyed, thus confirming our proposed mechanism.

-	~~{{STRUCTURE_1d06\| PDB=1d06 \| SCENE= }}~~	+	Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies.,Miyatake H, Mukai M, Park SY, Adachi S, Tamura K, Nakamura H, Nakamura K, Tsuchiya T, Iizuka T, Shiro Y J Mol Biol. 2000 Aug 11;301(2):415-31. PMID:10926518<ref>PMID:10926518</ref>

-	~~===STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10926518}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1d06]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1D06 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010926518<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Sinorhizobium meliloti]]		[[Category: Sinorhizobium meliloti]]
	[[Category: Adachi, S.]]		[[Category: Adachi, S.]]

OCA: Protected "1d06" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 20:54:44 GMT

Protected "1d06" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:54, 21 October 2012