4ofo - Revision history

OCA at 17:12, 20 September 2023

OCA — Wed, 20 Sep 2023 17:12:27 GMT

←Older revision		Revision as of 17:12, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OFO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OFO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [https://pdbe.org/4ofo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [https://www.ebi.ac.uk/pdbsum/4ofo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ofo 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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [https://pdbe.org/4ofo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [https://www.ebi.ac.uk/pdbsum/4ofo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ofo ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:22, 25 January 2023

OCA — Wed, 25 Jan 2023 07:22:34 GMT

←Older revision		Revision as of 07:22, 25 January 2023
Line 3:		Line 3:
	<StructureSection load='4ofo' size='340' side='right'caption='[[4ofo]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4ofo' size='340' side='right'caption='[[4ofo]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus~~ pestis~~" (lehmann and neumann 1896) migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4OFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OFO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ofl\|4ofl]]</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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [https://pdbe.org/4ofo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [https://www.ebi.ac.uk/pdbsum/4ofo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ofo ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oppA4, y1231, YP_2461, YPO2660 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [~~http~~://pdbe.org/4ofo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ofo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ofo ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2U2H355_YERPE A0A2U2H355_YERPE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cavazza, C~~]]	+	[[Category: Yersinia pestis]]
-	[[Category: ~~Lebrette, H~~]]	+	[[Category: Cavazza C]]
-	[[Category: ~~Abc-type importer]]~~	+	[[Category: Lebrette H]]
-	~~[[Category: Extracytoplasmic nickel-binding protein]]~~	+
-	~~[[Category: Nickel import]]~~	+
-	~~[[Category: Periplasmic]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 08:41, 10 April 2019

OCA — Wed, 10 Apr 2019 08:41:00 GMT

←Older revision		Revision as of 08:41, 10 April 2019
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	==Crystal structure of YntA from Yersinia pestis, unliganded form==		==Crystal structure of YntA from Yersinia pestis, unliganded form==
-	<StructureSection load='4ofo' size='340' side='right' caption='[[4ofo]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='4ofo' size='340' side='right'caption='[[4ofo]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OFO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OFO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ofl\|4ofl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ofl\|4ofl]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">oppA4, y1231, YP_2461, YPO2660 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [http://pdbe.org/4ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [http://www.ebi.ac.uk/pdbsum/4ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ofo 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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [http://pdbe.org/4ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [http://www.ebi.ac.uk/pdbsum/4ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ofo ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Cavazza, C]]		[[Category: Cavazza, C]]
	[[Category: Lebrette, H]]		[[Category: Lebrette, H]]

OCA at 21:00, 11 August 2016

OCA — Thu, 11 Aug 2016 21:00:35 GMT

←Older revision		Revision as of 21:00, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of YntA from Yersinia pestis, unliganded form==		==Crystal structure of YntA from Yersinia pestis, unliganded form==
	<StructureSection load='4ofo' size='340' side='right' caption='[[4ofo]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4ofo' size='340' side='right' caption='[[4ofo]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ofl\|4ofl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ofl\|4ofl]]</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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [http://www.ebi.ac.uk/pdbsum/4ofo 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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [http://pdbe.org/4ofo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [http://www.ebi.ac.uk/pdbsum/4ofo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ofo 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 4ofo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:21, 19 November 2014

OCA — Wed, 19 Nov 2014 09:21:24 GMT

←Older revision		Revision as of 09:21, 19 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OFO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OFO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ofl\|4ofl]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ofl\|4ofl]]</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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [http://www.ebi.ac.uk/pdbsum/4ofo 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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [http://www.ebi.ac.uk/pdbsum/4ofo 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 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cavazza, C.]]	+	[[Category: Cavazza, C]]
-	[[Category: Lebrette, H.]]	+	[[Category: Lebrette, H]]
	[[Category: Abc-type importer]]		[[Category: Abc-type importer]]
	[[Category: Extracytoplasmic nickel-binding protein]]		[[Category: Extracytoplasmic nickel-binding protein]]

OCA at 00:11, 2 October 2014

OCA — Thu, 02 Oct 2014 00:11:38 GMT

←Older revision		Revision as of 00:11, 2 October 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of YntA from Yersinia pestis, unliganded form==
		+	<StructureSection load='4ofo' size='340' side='right' caption='[[4ofo]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ofo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OFO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OFO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ofl\|4ofl]]</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=4ofo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ofo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ofo RCSB], [http://www.ebi.ac.uk/pdbsum/4ofo PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass that involves an extracytoplasmic nickel-binding protein, Ni-BP. This study reports on the structure of three Ni-BPs from a diversity of human pathogens and on the existence of three new nickel-binding motifs. These are different from that previously described for Escherichia coli Ni-BP NikA, known to bind nickel via a nickelophore, and indicate a variegated ligand selectivity for Ni-BPs. The structures are consistent with ligand affinities measured in solution by calorimetry and challenge the hypothesis of a general requirement of nickelophores for nickel uptake by canonical ABC importers. Phylogenetic analyses showed that Ni-BPs have different evolutionary origins and emerged independently from peptide-binding proteins, possibly explaining the promiscuous behavior of this class of Ni(II) carriers.

-	~~The entry 4ofo is ON HOLD until Paper Publication~~	+	Promiscuous Nickel Import in Human Pathogens: Structure, Thermodynamics, and Evolution of Extracytoplasmic Nickel-Binding Proteins.,Lebrette H, Brochier-Armanet C, Zambelli B, de Reuse H, Borezee-Durant E, Ciurli S, Cavazza C Structure. 2014 Sep 3. pii: S0969-2126(14)00243-3. doi:, 10.1016/j.str.2014.07.012. PMID:25199691<ref>PMID:25199691</ref>

-	~~Authors: Lebrette~~, H., Cavazza, C.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of YntA from Yersinia pestis~~, ~~unliganded form~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cavazza, C.]]
		+	[[Category: Lebrette, H.]]
		+	[[Category: Abc-type importer]]
		+	[[Category: Extracytoplasmic nickel-binding protein]]
		+	[[Category: Nickel import]]
		+	[[Category: Periplasmic]]
		+	[[Category: Transport protein]]

OCA at 06:15, 30 April 2014

OCA — Wed, 30 Apr 2014 06:15:56 GMT

←Older revision		Revision as of 06:15, 30 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Lebrette, H., Cavazza, C.		Authors: Lebrette, H., Cavazza, C.

	Description: Crystal structure of YntA from Yersinia pestis, unliganded form		Description: Crystal structure of YntA from Yersinia pestis, unliganded form

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

OCA — Wed, 22 Jan 2014 06:48:33 GMT

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

←Older revision

Revision as of 06:48, 22 January 2014

OCA: New page: '''Unreleased structure''' The entry 4ofo is ON HOLD Authors: Lebrette, H., Cavazza, C. Description: Crystal structure of YntA from Yersinia pestis, unliganded form

OCA — Wed, 22 Jan 2014 06:48:32 GMT

New page: '''Unreleased structure''' The entry 4ofo is ON HOLD Authors: Lebrette, H., Cavazza, C. Description: Crystal structure of YntA from Yersinia pestis, unliganded form

New page

'''Unreleased structure'''

The entry 4ofo is ON HOLD

Authors: Lebrette, H., Cavazza, C.

Description: Crystal structure of YntA from Yersinia pestis, unliganded form