1y28 - Revision history

OCA at 08:09, 25 October 2023

OCA — Wed, 25 Oct 2023 08:09:57 GMT

←Older revision		Revision as of 08:09, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1y28' size='340' side='right'caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1y28' size='340' side='right'caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium~~ japonicum~~" kirchner 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y28 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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]~~<~~/div></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~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">FIXL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])~~</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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [https://pdbe.org/1y28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [https://www.ebi.ac.uk/pdbsum/1y28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y28 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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [https://pdbe.org/1y28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [https://www.ebi.ac.uk/pdbsum/1y28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y28 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~FIXL_BRAJA FIXL_BRAJA~~]~~] 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_BRADU FIXL_BRADU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhizobacterium~~ japonicum ~~kirchner 1896~~]]	+	[[Category: Bradyrhizobium japonicum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dioum~~, E M~~]]	+	[[Category: Dioum EM]]
-	[[Category: Dunham~~, C M~~]]	+	[[Category: Dunham CM]]
-	[[Category: Gilles-Gonzalez~~, M A~~]]	+	[[Category: Gilles-Gonzalez MA]]
-	[[Category: Gonzalez, G]]	+	[[Category: Gonzalez G]]
-	[[Category: Scott~~, W G~~]]	+	[[Category: Scott WG]]
-	[[Category: Tuckerman~~, J R]]~~	+	[[Category: Tuckerman JR]]
-	~~[[Category: Oxygen sensing]]~~	+
-	~~[[Category: Pas fold]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:41, 10 November 2021

OCA — Wed, 10 Nov 2021 06:41:01 GMT

←Older revision		Revision as of 06:41, 10 November 2021
Line 3:		Line 3:
	<StructureSection load='1y28' size='340' side='right'caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1y28' size='340' side='right'caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y28 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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [~~http~~://pdbe.org/1y28 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1y28 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1y28 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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [https://pdbe.org/1y28 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [https://www.ebi.ac.uk/pdbsum/1y28 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y28 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FIXL_BRAJA FIXL_BRAJA]] 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_BRAJA FIXL_BRAJA]] 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 10:30, 6 January 2021

OCA — Wed, 06 Jan 2021 10:30:26 GMT

←Older revision		Revision as of 10:30, 6 January 2021
Line 1:		Line 1:

	==Crystal structure of the R220A metBJFIXL HEME domain==		==Crystal structure of the R220A metBJFIXL HEME domain==
-	<StructureSection load='1y28' size='340' side='right' caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1y28' size='340' side='right'caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Y28 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://pdbe.org/1y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y28 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://pdbe.org/1y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y28 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Rhizobacterium japonicum kirchner 1896]]		[[Category: Rhizobacterium japonicum kirchner 1896]]
		+	[[Category: Large Structures]]
	[[Category: Dioum, E M]]		[[Category: Dioum, E M]]
	[[Category: Dunham, C M]]		[[Category: Dunham, C M]]

OCA at 07:40, 18 April 2018

OCA — Wed, 18 Apr 2018 07:40:04 GMT

←Older revision		Revision as of 07:40, 18 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of the R220A metBJFIXL HEME domain==		==Crystal structure of the R220A metBJFIXL HEME domain==
	<StructureSection load='1y28' size='340' side='right' caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1y28' size='340' side='right' caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://pdbe.org/1y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://pdbe.org/1y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y28 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y2/1y28_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y2/1y28_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 21:26, 9 February 2016

OCA — Tue, 09 Feb 2016 21:26:30 GMT

←Older revision		Revision as of 21:26, 9 February 2016
Line 18:		Line 18:
	<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=1y28 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:11, 11 September 2015

OCA — Fri, 11 Sep 2015 02:11:41 GMT

←Older revision		Revision as of 02:11, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1y28' size='340' side='right' caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1y28' size='340' side='right' caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bradyrhizobium_japonicum Bradyrhizobium~~ japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y28 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y28 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 ~~Bradyrhizobium~~ japonicum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 "Rhizobacterium japonicum" Kirchner 1896])</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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://pdbe.org/1y28 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1y28" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bradyrhizobium~~ japonicum]]	+	[[Category: Rhizobacterium japonicum kirchner 1896]]
	[[Category: Dioum, E M]]		[[Category: Dioum, E M]]
	[[Category: Dunham, C M]]		[[Category: Dunham, C M]]

OCA at 09:38, 25 December 2014

OCA — Thu, 25 Dec 2014 09:38:56 GMT

←Older revision		Revision as of 09:38, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y28 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y28 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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 Bradyrhizobium japonicum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 Bradyrhizobium japonicum])</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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FIXL_BRAJA FIXL_BRAJA]] 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 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
-	[[Category: Dioum, E M.]]	+	[[Category: Dioum, E M]]
-	[[Category: Dunham, C M.]]	+	[[Category: Dunham, C M]]
-	[[Category: Gilles-Gonzalez, M A.]]	+	[[Category: Gilles-Gonzalez, M A]]
-	[[Category: Gonzalez, G.]]	+	[[Category: Gonzalez, G]]
-	[[Category: Scott, W G.]]	+	[[Category: Scott, W G]]
-	[[Category: Tuckerman, J R.]]	+	[[Category: Tuckerman, J R]]
	[[Category: Oxygen sensing]]		[[Category: Oxygen sensing]]
	[[Category: Pas fold]]		[[Category: Pas fold]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 20:44, 29 September 2014

OCA — Mon, 29 Sep 2014 20:44:34 GMT

←Older revision		Revision as of 20:44, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1y28.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the R220A metBJFIXL HEME domain==
		+	<StructureSection load='1y28' size='340' side='right' caption='[[1y28]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1y28]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y28 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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d06\|1d06]], [[1dp6\|1dp6]], [[1dp8\|1dp8]], [[1dp9\|1dp9]], [[1drm\|1drm]], [[1lsv\|1lsv]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FIXL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=375 Bradyrhizobium japonicum])</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=1y28 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y28 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y28 RCSB], [http://www.ebi.ac.uk/pdbsum/1y28 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/y2/1y28_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 ==
		+	To evaluate the contributions of the G(beta)-2 arginine to signal transduction in oxygen-sensing heme-PAS domains, we replaced this residue with alanine in Bradyrhizobium japonicum FixL and examined the results on heme-domain structure, ligand binding, and kinase regulation. In the isolated R220A BjFixL heme-PAS domain, the iron-histidine bond was increased in length by 0.31 A, the heme flattened even without a ligand, and the interaction of a presumed regulatory loop (the FG loop) with the helix of heme attachment was weakened. Binding of carbon monoxide was similar for ferrous BjFixL and R220A BjFixL. In contrast, the level of binding of oxygen was dramatically lower (K(d) approximately 1.5 mM) for R220A BjFixL, and this was manifested as 60- and 3-fold lower on- and off-rate constants, respectively. Binding of cyanide followed the same pattern as binding of oxygen. The catalytic activity was 3-4-fold higher in the "on-state" unliganded forms of R220A BjFixL than in the corresponding BjFixL species. Cyanide regulation of this activity was strongly impaired, but some inhibition was nevertheless preserved. Carbon monoxide and nitric oxide regulation, although weak in BjFixL, were abolished from R220A BjFixL. We conclude that the G(beta)-2 arginine assists in the binding of oxygen to BjFixL but does not accomplish this by stabilizing the oxy form. This arginine is not absolutely required for regulation, although it is important for shifting a pre-existing kinase equilibrium toward the inactive state on binding of regulatory ligands. These findings support a regulatory model in which the heme-PAS domain operates as an ensemble that couples to the kinase rather than a mechanism driven by a single central switch.

-	~~{{STRUCTURE_1y28\| PDB=1y28 \| SCENE= }}~~	+	A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure.,Dunham CM, Dioum EM, Tuckerman JR, Gonzalez G, Scott WG, Gilles-Gonzalez MA Biochemistry. 2003 Jul 1;42(25):7701-8. PMID:12820879<ref>PMID:12820879</ref>

-	~~===Crystal structure~~ of the ~~R220A metBJFIXL HEME domain===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12820879}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1y28]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012820879<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Dioum, E M.]]		[[Category: Dioum, E M.]]

OCA: Protected "1y28" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:35:28 GMT

Protected "1y28" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:35, 5 January 2013

OCA at 11:35, 5 January 2013

OCA — Sat, 05 Jan 2013 11:35:26 GMT

←Older revision		Revision as of 11:35, 5 January 2013
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-	{{Seed}}
	[[Image:1y28.png\|left\|200px]]		[[Image:1y28.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1y28", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_1y28\| PDB=1y28 \| SCENE= }}		{{STRUCTURE_1y28\| PDB=1y28 \| SCENE= }}

	===Crystal structure of the R220A metBJFIXL HEME domain===		===Crystal structure of the R220A metBJFIXL HEME domain===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12820879}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12820879 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12820879}}		{{ABSTRACT_PUBMED_12820879}}

	==About this Structure==		==About this Structure==
-	~~1Y28~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA].	+	[[1y28]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y28 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12820879~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012820879</ref><references group="xtra"/>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Dioum, E M.]]		[[Category: Dioum, E M.]]
Line 33:		Line 21:
	[[Category: Oxygen sensing]]		[[Category: Oxygen sensing]]
	[[Category: Pas fold]]		[[Category: Pas fold]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 12:52:30 2009''~~	+