4d6y - Revision history

OCA at 12:21, 20 December 2023

2023-12-20T12:21:48Z

←Older revision		Revision as of 12:21, 20 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_abortus Brucella abortus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_abortus Brucella abortus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [https://pdbe.org/4d6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [https://www.ebi.ac.uk/pdbsum/4d6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d6y 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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [https://pdbe.org/4d6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [https://www.ebi.ac.uk/pdbsum/4d6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d6y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q2YPW6_BRUA2 Q2YPW6_BRUA2]]	+	[https://www.uniprot.org/uniprot/Q2YPW6_BRUA2 Q2YPW6_BRUA2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:50, 14 September 2022

2022-09-14T07:50:15Z

←Older revision		Revision as of 07:50, 14 September 2022
Line 3:		Line 3:
	<StructureSection load='4d6y' size='340' side='right'caption='[[4d6y]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4d6y' size='340' side='right'caption='[[4d6y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacterium_abortus"_schmidt_in_schmidt_and_weis_1901 "bacterium~~ abortus~~" schmidt in schmidt and weis 1901~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_abortus Brucella abortus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [~~http~~://pdbe.org/4d6y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4d6y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4d6y 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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [https://pdbe.org/4d6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [https://www.ebi.ac.uk/pdbsum/4d6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d6y ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q2YPW6_BRUA2 Q2YPW6_BRUA2]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ abortus ~~schmidt in schmidt and weis 1901~~]]	+	[[Category: Brucella abortus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carrica~~, M C~~]]	+	[[Category: Carrica MC]]
-	[[Category: Fernandez, I]]	+	[[Category: Fernandez I]]
-	[[Category: Goldbaum~~, F A~~]]	+	[[Category: Goldbaum FA]]
-	[[Category: Klinke, S]]	+	[[Category: Klinke S]]
-	[[Category: Otero~~, L H]]~~	+	[[Category: Otero LH]]
-	~~[[Category: Brucellosis]]~~	+
-	~~[[Category: Microaerobisis]]~~	+
-	~~[[Category: Rec domain]]~~	+
-	~~[[Category: Response regulator]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Two-component system~~]]	+

OCA at 07:34, 27 March 2019

2019-03-27T07:34:53Z

←Older revision		Revision as of 07:34, 27 March 2019
Line 1:		Line 1:
		+
	==Crystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium==		==Crystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium==
-	<StructureSection load='4d6y' size='340' side='right' caption='[[4d6y]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4d6y' size='340' side='right'caption='[[4d6y]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_abortus"_schmidt_in_schmidt_and_weis_1901 "bacterium abortus" schmidt in schmidt and weis 1901]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [http://pdbe.org/4d6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [http://www.ebi.ac.uk/pdbsum/4d6y 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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [http://pdbe.org/4d6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [http://www.ebi.ac.uk/pdbsum/4d6y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d6y ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium abortus schmidt in schmidt and weis 1901]]
		+	[[Category: Large Structures]]
	[[Category: Carrica, M C]]		[[Category: Carrica, M C]]
	[[Category: Fernandez, I]]		[[Category: Fernandez, I]]

OCA at 07:27, 7 October 2015

2015-10-07T07:27:07Z

←Older revision		Revision as of 07:27, 7 October 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [http://www.ebi.ac.uk/pdbsum/4d6y 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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [http://pdbe.org/4d6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [http://www.ebi.ac.uk/pdbsum/4d6y PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	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 4d6y" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:44, 8 July 2015

2015-07-08T14:44:46Z

←Older revision		Revision as of 14:44, 8 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium==
		+	<StructureSection load='4d6y' size='340' side='right' caption='[[4d6y]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4d6y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D6Y FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d6y RCSB], [http://www.ebi.ac.uk/pdbsum/4d6y PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Brucella abortus is an important pathogenic bacterium that has to overcome oxygen deficiency in order to achieve a successful infection. Previously, we proved that a two-component system formed by the histidine kinase NtrY and the response regulator NtrX is essential to achieve an adaptive response to low oxygen tension conditions. Even though the relevance of this signaling pathway has already been demonstrated in other microorganisms, its molecular activation mechanism has not yet been described in detail. In this article, we report the first crystal structures from different conformations of the NtrX receiver domain from B. abortus, and we propose a sequence of events to explain the structural rearrangements along the activation process. The analysis of the structures obtained in the presence of the phosphoryl group analog beryllofluoride led us to postulate that changes in the interface formed by the alpha4 helix and the beta5 strand are important for the activation, producing a reorientation of the alpha5 helix. Also, a biochemical characterization of the NtrX receiver domain enzymatic activities was performed, describing its autophosphorylation and autodephosphorylation kinetics. Finally, the role of H85, an important residue, was addressed by site-directed mutagenesis. Overall, these results provide significant structural basis for understanding the response regulator activation in this bacterial two-component system.

-	~~The entry 4d6y is ON HOLD until Paper Publication~~	+	Snapshots of Conformational Changes Shed Light into the NtrX Receiver Domain Signal Transduction Mechanism.,Fernandez I, Otero LH, Klinke S, Carrica MD, Goldbaum FA J Mol Biol. 2015 Jun 23. pii: S0022-2836(15)00350-2. doi:, 10.1016/j.jmb.2015.06.010. PMID:26113057<ref>PMID:26113057</ref>

-	~~Authors: Otero~~, L.~~H., Fernandez, I., Carrica, M.C., Klinke,~~ S.~~, Goldbaum, F.A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	[[Category: Carrica, M.C]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Carrica, M C]]
	[[Category: Fernandez, I]]		[[Category: Fernandez, I]]
		+	[[Category: Goldbaum, F A]]
	[[Category: Klinke, S]]		[[Category: Klinke, S]]
-	[[Category: ~~Goldbaum~~, ~~F.A~~]]	+	[[Category: Otero, L H]]
-	[[Category: ~~Otero, L.H~~]]	+	[[Category: Brucellosis]]
		+	[[Category: Microaerobisis]]
		+	[[Category: Rec domain]]
		+	[[Category: Response regulator]]
		+	[[Category: Signaling protein]]
		+	[[Category: Two-component system]]

OCA at 13:54, 24 December 2014

2014-12-24T13:54:50Z

←Older revision		Revision as of 13:54, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium		Description: Crystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium
		+	[[Category: Unreleased Structures]]
		+	[[Category: Carrica, M.C]]
		+	[[Category: Fernandez, I]]
		+	[[Category: Klinke, S]]
		+	[[Category: Goldbaum, F.A]]
		+	[[Category: Otero, L.H]]

OCA: Protected "4d6y" [edit=sysop:move=sysop]

2014-11-26T06:27:18Z

Protected "4d6y" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:27, 26 November 2014

OCA: New page: '''Unreleased structure''' The entry 4d6y is ON HOLD until Paper Publication Authors: Otero, L.H., Fernandez, I., Carrica, M.C., Klinke, S., Goldbaum, F.A. Description: Crystal structu...

2014-11-26T06:27:17Z

New page: '''Unreleased structure''' The entry 4d6y is ON HOLD until Paper Publication Authors: Otero, L.H., Fernandez, I., Carrica, M.C., Klinke, S., Goldbaum, F.A. Description: Crystal structu...

New page

'''Unreleased structure'''

The entry 4d6y is ON HOLD until Paper Publication

Authors: Otero, L.H., Fernandez, I., Carrica, M.C., Klinke, S., Goldbaum, F.A.

Description: Crystal structure of the receiver domain of NtrX from Brucella abortus in complex with beryllofluoride and magnesium