6oby - Revision history

OCA at 12:56, 6 November 2024

2024-11-06T12:56:50Z

← Older revision		Revision as of 12:56, 6 November 2024
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	<StructureSection load='6oby' size='340' side='right'caption='[[6oby]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='6oby' size='340' side='right'caption='[[6oby]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6oby]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arcfl Arcfl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OBY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6oby]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OBY FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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]] 2.87Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td~~></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~[[3kb1\|3kb1]]~~</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=6oby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oby OCA], [https://pdbe.org/6oby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oby RCSB], [https://www.ebi.ac.uk/pdbsum/6oby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oby 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=6oby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oby OCA], [~~http~~://pdbe.org/6oby PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6oby RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6oby PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6oby ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/O28015_ARCFU O28015_ARCFU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Arcfl~~]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Garman~~, E F~~]]		[[Category: Garman EF]]
	[[Category: Lowe~~, E D~~]]		[[Category: Lowe ED]]
	[[Category: Snell~~, E H]]~~		[[Category: Snell EH]]
	~~[[Category: Alpha-beta protein]]~~
	~~[[Category: Metal transport]]~~
	~~[[Category: Pixe~~]]

OCA at 09:24, 8 January 2020

2020-01-08T09:24:50Z

← Older revision		Revision as of 09:24, 8 January 2020
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	<StructureSection load='6oby' size='340' side='right'caption='[[6oby]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='6oby' size='340' side='right'caption='[[6oby]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6oby]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OBY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6oby]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OBY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Arcfl]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Garman, E F]]		[[Category: Garman, E F]]

OCA at 09:09, 25 December 2019

2019-12-25T09:09:25Z

← Older revision		Revision as of 09:09, 25 December 2019
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	~~'''Unreleased structure'''~~

	The ~~entry~~ 6oby is ~~ON HOLD~~		==The nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE. Based on 3KB1.==
			<StructureSection load='6oby' size='340' side='right'caption='[[6oby]], [[Resolution\|resolution]] 2.87Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[6oby]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OBY FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kb1\|3kb1]]</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=6oby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oby OCA], [http://pdbe.org/6oby PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oby RCSB], [http://www.ebi.ac.uk/pdbsum/6oby PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oby ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Metalloproteins comprise over one-third of proteins, with approximately half of all enzymes requiring metal to function. Accurate identification of these metal atoms and their environment is a prerequisite to understanding biological mechanism. Using ion beam analysis through particle induced X-ray emission (PIXE), we have quantitatively identified the metal atoms in 30 previously structurally characterized proteins using minimal sample volume and a high-throughput approach. Over half of these metals had been misidentified in the deposited structural models. Some of the PIXE detected metals not seen in the models were explainable as artifacts from promiscuous crystallization reagents. For others, using the correct metal improved the structural models. For multinuclear sites, anomalous diffraction signals enabled the positioning of the correct metals to reveal previously obscured biological information. PIXE is insensitive to the chemical environment, but coupled with experimental diffraction data deposited alongside the structural model it enables validation and potential remediation of metalloprotein models, improving structural and, more importantly, mechanistic knowledge.

	~~Authors~~: Snell, ~~E.H.~~, Garman~~, E~~.F.~~, Lowe, E~~.D.		High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application.,Grime GW, Zeldin OB, Snell ME, Lowe ED, Hunt JF, Montelione GT, Tong L, Snell EH, Garman EF J Am Chem Soc. 2019 Dec 20. doi: 10.1021/jacs.9b09186. PMID:31794207<ref>PMID:31794207</ref>

	~~Description: The nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE~~. ~~Based on 3KB1~~.		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: Garman, E.F]]		<div class="pdbe-citations 6oby" style="background-color:#fffaf0;"></div>
	[[Category: Lowe, E.D]]		== References ==
	[[Category: Snell, E.H]]		<references/>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Garman, E F]]
			[[Category: Lowe, E D]]
			[[Category: Snell, E H]]
			[[Category: Alpha-beta protein]]
			[[Category: Metal transport]]
			[[Category: Pixe]]

OCA: Protected "6oby" [edit=sysop:move=sysop]

2019-03-27T05:07:34Z

Protected "6oby" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:07, 27 March 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6oby is ON HOLD Authors: Snell, E.H., Garman, E.F., Lowe, E.D. Description: The nucleotide-binding protein AF_226 in complex with ADP from Archaeog...

2019-03-27T05:07:33Z

New page: '''Unreleased structure''' The entry 6oby is ON HOLD Authors: Snell, E.H., Garman, E.F., Lowe, E.D. Description: The nucleotide-binding protein AF_226 in complex with ADP from Archaeog...

New page

'''Unreleased structure'''

The entry 6oby is ON HOLD

Authors: Snell, E.H., Garman, E.F., Lowe, E.D.

Description: The nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE. Based on 3KB1.
[[Category: Unreleased Structures]]
[[Category: Garman, E.F]]
[[Category: Lowe, E.D]]
[[Category: Snell, E.H]]