4evb - Revision history

OCA at 13:49, 8 November 2023

2023-11-08T13:49:47Z

←Older revision		Revision as of 13:49, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4evb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4evb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EVB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4evb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4evb OCA], [https://pdbe.org/4evb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4evb RCSB], [https://www.ebi.ac.uk/pdbsum/4evb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4evb 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=4evb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4evb OCA], [https://pdbe.org/4evb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4evb RCSB], [https://www.ebi.ac.uk/pdbsum/4evb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4evb ProSAT]</span></td></tr>
	</table>		</table>

OCA at 04:18, 7 October 2022

2022-10-07T04:18:21Z

←Older revision		Revision as of 04:18, 7 October 2022
Line 1:		Line 1:

	==Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)==		==Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)==
-	<StructureSection load='4evb' size='340' side='right' caption='[[4evb]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4evb' size='340' side='right'caption='[[4evb]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4evb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43504 Atcc 43504~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4EVB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4evb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EVB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ta8\|3ta8]], [[3t9j\|3t9j]], [[4evc\|4evc]], [[4evd\|4evd]], [[4eve\|4eve]]</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=4evb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4evb OCA], [https://pdbe.org/4evb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4evb RCSB], [https://www.ebi.ac.uk/pdbsum/4evb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4evb ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">napA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])~~</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=4evb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4evb OCA], [~~http~~://pdbe.org/4evb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4evb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4evb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4evb ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G1UIZ3_HELPX G1UIZ3_HELPX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 43504~~]]	+	[[Category: Helicobacter pylori]]
-	[[Category: Akao, N]]	+	[[Category: Large Structures]]
-	[[Category: Fujii, S]]	+	[[Category: Akao N]]
-	[[Category: Tsuruta, O]]	+	[[Category: Fujii S]]
-	[[Category: Yokoyama, H]]	+	[[Category: Tsuruta O]]
-	~~[[Category: Dodecamer]]~~	+	[[Category: Yokoyama H]]
-	~~[[Category: Four-helix bundle]]~~	+
-	~~[[Category: Metal transport~~]]	+

OCA at 15:09, 11 August 2016

2016-08-11T15:09:21Z

←Older revision		Revision as of 15:09, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)==		==Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)==
	<StructureSection load='4evb' size='340' side='right' caption='[[4evb]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4evb' size='340' side='right' caption='[[4evb]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4evb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Helicobacter_pylori Helicobacter pylori~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EVB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4evb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EVB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ta8\|3ta8]], [[3t9j\|3t9j]], [[4evc\|4evc]], [[4evd\|4evd]], [[4eve\|4eve]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ta8\|3ta8]], [[3t9j\|3t9j]], [[4evc\|4evc]], [[4evd\|4evd]], [[4eve\|4eve]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">napA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ~~Helicobacter pylori~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">napA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</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=4evb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4evb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4evb RCSB], [http://www.ebi.ac.uk/pdbsum/4evb 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=4evb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4evb OCA], [http://pdbe.org/4evb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4evb RCSB], [http://www.ebi.ac.uk/pdbsum/4evb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4evb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4evb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Helicobacter pylori~~]]	+	[[Category: Atcc 43504]]
	[[Category: Akao, N]]		[[Category: Akao, N]]
	[[Category: Fujii, S]]		[[Category: Fujii, S]]

OCA at 13:42, 4 January 2015

2015-01-04T13:42:16Z

←Older revision		Revision as of 13:42, 4 January 2015
Line 1:		Line 1:
-	[[~~Image:~~4evb.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)==
		+	<StructureSection load='4evb' size='340' side='right' caption='[[4evb]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4evb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EVB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ta8\|3ta8]], [[3t9j\|3t9j]], [[4evc\|4evc]], [[4evd\|4evd]], [[4eve\|4eve]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">napA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori])</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=4evb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4evb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4evb RCSB], [http://www.ebi.ac.uk/pdbsum/4evb PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Helicobacter pylori neutrophil-activating protein (HP-NAP) is a Dps-like iron storage protein forming a dodecameric shell, and promotes adhesion of neutrophils to endothelial cells. The crystal structure of HP-NAP in a Zn(2+)- or Cd(2+)-bound form reveals the binding of two zinc or two cadmium ions and their bridged water molecule at the ferroxidase center (FOC). The two zinc ions are coordinated in a tetrahedral manner to the conserved residues among HP-NAP and Dps proteins. The two cadmium ions are coordinated in a trigonal-bipyramidal and distorted octahedral manner. In both structures, the second ion is more weakly coordinated than the first. Another zinc ion is found inside of the negatively-charged threefold-related pore, which is suitable for metal ions to pass through.

-	~~{{STRUCTURE_4evb\| PDB=4evb \| SCENE= }}~~	+	Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form.,Yokoyama H, Tsuruta O, Akao N, Fujii S Biochem Biophys Res Commun. 2012 Jun 15;422(4):745-50. Epub 2012 May 19. PMID:22618234<ref>PMID:22618234</ref>

-	~~===Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22618234}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[4evb]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Helicobacter_pylori Helicobacter pylori]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022618234<~~/~~ref~~><~~ref group="xtra">PMID:022297984</ref><references group="xtra"~~/>	+
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
-	[[Category: Akao, N.]]	+	[[Category: Akao, N]]
-	[[Category: Fujii, S.]]	+	[[Category: Fujii, S]]
-	[[Category: Tsuruta, O.]]	+	[[Category: Tsuruta, O]]
-	[[Category: Yokoyama, H.]]	+	[[Category: Yokoyama, H]]
	[[Category: Dodecamer]]		[[Category: Dodecamer]]
	[[Category: Four-helix bundle]]		[[Category: Four-helix bundle]]
	[[Category: Metal transport]]		[[Category: Metal transport]]

OCA at 05:48, 27 June 2012

2012-06-27T05:48:50Z

←Older revision		Revision as of 05:48, 27 June 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4evb.jpg\|left\|200px]]

-	~~The entry~~ 4evb ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4evb\| PDB=4evb \| SCENE= }}

-	~~Authors: Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.~~	+	===Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)===

-	~~Description: Crystal~~ Structure ~~HP-NAP~~ from ~~strain YS39 zinc soaked (20mM)~~	+	{{ABSTRACT_PUBMED_22618234}}
		+
		+	==About this Structure==
		+	[[4evb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EVB OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022618234</ref><ref group="xtra">PMID:022297984</ref><references group="xtra"/>
		+	[[Category: Helicobacter pylori]]
		+	[[Category: Akao, N.]]
		+	[[Category: Fujii, S.]]
		+	[[Category: Tsuruta, O.]]
		+	[[Category: Yokoyama, H.]]
		+	[[Category: Dodecamer]]
		+	[[Category: Four-helix bundle]]
		+	[[Category: Metal transport]]

OCA at 05:29, 30 May 2012

2012-05-30T05:29:13Z

←Older revision		Revision as of 05:29, 30 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.		Authors: Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.

	Description: Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)		Description: Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)

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

2012-05-02T19:00:48Z

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

←Older revision

Revision as of 19:00, 2 May 2012

OCA: New page: '''Unreleased structure''' The entry 4evb is ON HOLD Authors: Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S. Description: Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)

2012-05-02T19:00:47Z

New page: '''Unreleased structure''' The entry 4evb is ON HOLD Authors: Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S. Description: Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)

New page

'''Unreleased structure'''

The entry 4evb is ON HOLD

Authors: Yokoyama, H., Tsuruta, O., Akao, N., Fujii, S.

Description: Crystal Structure HP-NAP from strain YS39 zinc soaked (20mM)