5ggx - Revision history

OCA at 11:31, 2 August 2023

OCA — Wed, 02 Aug 2023 11:31:18 GMT

←Older revision		Revision as of 11:31, 2 August 2023
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	<StructureSection load='5ggx' size='340' side='right'caption='[[5ggx]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='5ggx' size='340' side='right'caption='[[5ggx]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ggx]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Vibc3 Vibc3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GGX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ggx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O395 Vibrio cholerae O395]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GGX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DEF:DEFEROXAMINE+MESYLATE+FE(III)+COMPLEX'>DEF</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]] 3.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5ggy\|5ggy]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DEF:DEFEROXAMINE+MESYLATE+FE(III)+COMPLEX'>DEF</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">VC0395_A2582 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=345073 VIBC3])~~</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=5ggx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ggx OCA], [https://pdbe.org/5ggx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ggx RCSB], [https://www.ebi.ac.uk/pdbsum/5ggx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ggx 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=5ggx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ggx OCA], [~~http~~://pdbe.org/5ggx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ggx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ggx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ggx ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A0H3AJ03_VIBC3 A0A0H3AJ03_VIBC3]
-	The mechanism of haem transport across the inner membrane of pathogenic bacteria is currently insufficiently understood at the molecular level and no information is available for this process in Vibrio cholerae. To obtain structural insights into the periplasmic haem-binding protein HutB from V. cholerae (VcHutB), which is involved in haem transport through the HutBCD haem-transport system, at the atomic level, VcHutB was cloned, overexpressed and crystallized using 1.6 M ammonium sulfate as a precipitant at pH 7.0. X-ray diffraction data were collected to 2.4 A resolution on the RRCAT PX-BL-21 beamline at the Indus-2 synchrotron, Indore, India. The crystals belonged to space group P4(3)2(1)2, with unit-cell parameters a = b = 62.88, c = 135.8 A. Matthews coefficient calculations indicated the presence of one monomer in the asymmetric unit, with an approximate solvent content of 45.02%. Molecular-replacement calculations with Phaser confirmed the presence of a monomer in the asymmetric unit.	+
-		+
-	Purification, crystallization and preliminary X-ray analysis of the periplasmic haem-binding protein HutB from Vibrio cholerae.,Agarwal S, Biswas M, Dasgupta J Acta Crystallogr F Struct Biol Commun. 2015 Apr;71(Pt 4):~~401-4. doi:, 10.1107~~/~~S2053230X15003660. Epub 2015 Mar 20. PMID:25849499<ref>PMID:25849499<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5ggx" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Vibc3~~]]	+	[[Category: Vibrio cholerae O395]]
-	[[Category: Agarwal, S]]	+	[[Category: Agarwal S]]
-	[[Category: Dasgupta, J]]	+	[[Category: Dasgupta J]]
-	[[Category: Dey, S]]	+	[[Category: Dey S]]
-	[[Category: Ghosh, B]]	+	[[Category: Ghosh B]]
-	~~[[Category: Abc transporter]]~~	+
-	~~[[Category: Desferal]]~~	+
-	~~[[Category: Fhud]]~~	+
-	~~[[Category: Iron-siderophore]]~~	+
-	~~[[Category: Periplasmic protein]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Vibrio cholerae~~]]	+

OCA at 06:42, 13 May 2020

OCA — Wed, 13 May 2020 06:42:46 GMT

←Older revision		Revision as of 06:42, 13 May 2020
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	==Crystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio cholerae==		==Crystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio cholerae==
-	<StructureSection load='5ggx' size='340' side='right' caption='[[5ggx]], [[Resolution\|resolution]] 3.40Å' scene=''>	+	<StructureSection load='5ggx' size='340' side='right'caption='[[5ggx]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ggx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GGX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ggx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibc3 Vibc3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GGX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DEF:DEFEROXAMINE+MESYLATE+FE(III)+COMPLEX'>DEF</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DEF:DEFEROXAMINE+MESYLATE+FE(III)+COMPLEX'>DEF</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ggy\|5ggy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ggy\|5ggy]]</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=5ggx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ggx OCA], [http://pdbe.org/5ggx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ggx RCSB], [http://www.ebi.ac.uk/pdbsum/5ggx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ggx ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VC0395_A2582 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=345073 VIBC3])</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=5ggx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ggx OCA], [http://pdbe.org/5ggx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ggx RCSB], [http://www.ebi.ac.uk/pdbsum/5ggx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ggx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Vibc3]]
	[[Category: Agarwal, S]]		[[Category: Agarwal, S]]
	[[Category: Dasgupta, J]]		[[Category: Dasgupta, J]]

OCA at 01:31, 11 March 2017

OCA — Sat, 11 Mar 2017 01:31:19 GMT

←Older revision		Revision as of 01:31, 11 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ggx is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Fe3+ - Desferal bound siderophore binding protein FhuD from Vibrio cholerae==
		+	<StructureSection load='5ggx' size='340' side='right' caption='[[5ggx]], [[Resolution\|resolution]] 3.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ggx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GGX FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DEF:DEFEROXAMINE+MESYLATE+FE(III)+COMPLEX'>DEF</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ggy\|5ggy]]</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=5ggx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ggx OCA], [http://pdbe.org/5ggx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ggx RCSB], [http://www.ebi.ac.uk/pdbsum/5ggx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ggx ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The mechanism of haem transport across the inner membrane of pathogenic bacteria is currently insufficiently understood at the molecular level and no information is available for this process in Vibrio cholerae. To obtain structural insights into the periplasmic haem-binding protein HutB from V. cholerae (VcHutB), which is involved in haem transport through the HutBCD haem-transport system, at the atomic level, VcHutB was cloned, overexpressed and crystallized using 1.6 M ammonium sulfate as a precipitant at pH 7.0. X-ray diffraction data were collected to 2.4 A resolution on the RRCAT PX-BL-21 beamline at the Indus-2 synchrotron, Indore, India. The crystals belonged to space group P4(3)2(1)2, with unit-cell parameters a = b = 62.88, c = 135.8 A. Matthews coefficient calculations indicated the presence of one monomer in the asymmetric unit, with an approximate solvent content of 45.02%. Molecular-replacement calculations with Phaser confirmed the presence of a monomer in the asymmetric unit.

-	~~Authors: Agarwal~~, S., ~~Dey,~~ S., ~~Ghosh, B.~~, Dasgupta, J.	+	Purification, crystallization and preliminary X-ray analysis of the periplasmic haem-binding protein HutB from Vibrio cholerae.,Agarwal S, Biswas M, Dasgupta J Acta Crystallogr F Struct Biol Commun. 2015 Apr;71(Pt 4):401-4. doi:, 10.1107/S2053230X15003660. Epub 2015 Mar 20. PMID:25849499<ref>PMID:25849499</ref>

-	~~Description: Crystal Structure~~ of ~~Fe3+~~ -~~Desferal bound siderophore binding protein FhuD from Vibrio cholerae~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ggx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Agarwal, S]]
	[[Category: Dasgupta, J]]		[[Category: Dasgupta, J]]
	[[Category: Dey, S]]		[[Category: Dey, S]]
-	[[Category: Agarwal, S]]
	[[Category: Ghosh, B]]		[[Category: Ghosh, B]]
		+	[[Category: Abc transporter]]
		+	[[Category: Desferal]]
		+	[[Category: Fhud]]
		+	[[Category: Iron-siderophore]]
		+	[[Category: Periplasmic protein]]
		+	[[Category: Transport protein]]
		+	[[Category: Vibrio cholerae]]

OCA at 23:05, 3 August 2016

OCA — Wed, 03 Aug 2016 23:05:17 GMT

←Older revision		Revision as of 23:05, 3 August 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ggx is ON HOLD	+	The entry 5ggx is ON HOLD until Paper Publication

	Authors: Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.		Authors: Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.

OCA at 06:29, 14 July 2016

OCA — Thu, 14 Jul 2016 06:29:34 GMT

←Older revision		Revision as of 06:29, 14 July 2016
Line 5:		Line 5:
	Authors: Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.		Authors: Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.

-	Description: ~~Crsytsal~~ Structure of Fe3+ -Desferal bound siderophore binding protein FhuD from Vibrio cholerae	+	Description: Crystal Structure of Fe3+ -Desferal bound siderophore binding protein FhuD from Vibrio cholerae
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Dasgupta, J]]		[[Category: Dasgupta, J]]

OCA: Protected "5ggx" [edit=sysop:move=sysop]

OCA — Thu, 23 Jun 2016 18:42:34 GMT

Protected "5ggx" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:42, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5ggx is ON HOLD Authors: Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J. Description: Crsytsal Structure of Fe3+ -Desferal bound siderophore binding ...

OCA — Thu, 23 Jun 2016 18:42:33 GMT

New page: '''Unreleased structure''' The entry 5ggx is ON HOLD Authors: Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J. Description: Crsytsal Structure of Fe3+ -Desferal bound siderophore binding ...

New page

'''Unreleased structure'''

The entry 5ggx is ON HOLD

Authors: Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.

Description: Crsytsal Structure of Fe3+ -Desferal bound siderophore binding protein FhuD from Vibrio cholerae
[[Category: Unreleased Structures]]
[[Category: Dasgupta, J]]
[[Category: Dey, S]]
[[Category: Agarwal, S]]
[[Category: Ghosh, B]]