1vim - Revision history

OCA at 00:04, 28 December 2023

2023-12-28T00:04:14Z

← Older revision		Revision as of 00:04, 28 December 2023
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	<StructureSection load='1vim' size='340' side='right'caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='1vim' size='340' side='right'caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vim]] is a 4 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=1VIM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1VIM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vim]] is a 4 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=1VIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VIM FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 1.36Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~AF1796 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [~~http~~://pdbe.org/1vim PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1vim PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1vim 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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [https://pdbe.org/1vim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [https://www.ebi.ac.uk/pdbsum/1vim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vim ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Y1796_ARCFU Y1796_ARCFU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Arcfl~~]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: GenomiX~~, Structural]]~~		[[Category: Structural GenomiX]]
	~~[[Category: Structural genomic]]~~
	~~[[Category: Unknown function~~]]

OCA at 07:37, 30 December 2020

2020-12-30T07:37:34Z

← Older revision		Revision as of 07:37, 30 December 2020
Line 1:		Line 1:

	==Crystal structure of an hypothetical protein==		==Crystal structure of an hypothetical protein==
	<StructureSection load='1vim' size='340' side='right' caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='1vim' size='340' side='right'caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vim]] is a 4 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=1VIM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1VIM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vim]] is a 4 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=1VIM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1VIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://pdbe.org/1vim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vim 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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://pdbe.org/1vim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vim ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Arcfl]]		[[Category: Arcfl]]
			[[Category: Large Structures]]
	[[Category: GenomiX, Structural]]		[[Category: GenomiX, Structural]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 07:15, 4 April 2018

2018-04-04T07:15:39Z

← Older revision		Revision as of 07:15, 4 April 2018
Line 1:		Line 1:

	==Crystal structure of an hypothetical protein==		==Crystal structure of an hypothetical protein==
	<StructureSection load='1vim' size='340' side='right' caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='1vim' size='340' side='right' caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://pdbe.org/1vim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim 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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://pdbe.org/1vim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vim ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vi/1vim_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vi/1vim_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vim ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:20, 12 September 2015

2015-09-12T01:20:01Z

← Older revision		Revision as of 01:20, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1vim' size='340' side='right' caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='1vim' size='340' side='right' caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Archaeoglobus_fulgidus Archaeoglobus fulgidus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vim]] is a 4 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=1VIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ~~Archaeoglobus fulgidus~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim 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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://pdbe.org/1vim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 1vim" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Archaeoglobus fulgidus~~]]		[[Category: Arcfl]]
	[[Category: GenomiX, Structural]]		[[Category: GenomiX, Structural]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 12:22, 6 January 2015

2015-01-06T12:22:48Z

← Older revision		Revision as of 12:22, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIM FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim 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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: GenomiX, Structural.]]		[[Category: GenomiX, Structural]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 21:18, 29 September 2014

2014-09-29T21:18:21Z

← Older revision		Revision as of 21:18, 29 September 2014
Line 1:		Line 1:
	[[Image:~~1vim~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of an hypothetical protein==
			<StructureSection load='1vim' size='340' side='right' caption='[[1vim]], [[Resolution\|resolution]] 1.36Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1vim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VIM FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AF1796 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])</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=1vim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vim RCSB], [http://www.ebi.ac.uk/pdbsum/1vim PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vi/1vim_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

	~~{{STRUCTURE_1vim\| PDB=1vim \| SCENE= }}~~		Structural analysis of a set of proteins resulting from a bacterial genomics project.,Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ Proteins. 2005 Sep 1;60(4):787-96. PMID:16021622<ref>PMID:16021622</ref>

	~~===Crystal structure~~ of ~~an hypothetical protein===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16021622}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[1vim]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016021622<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: GenomiX, Structural.]]		[[Category: GenomiX, Structural.]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA: Protected "1vim" [edit=sysop:move=sysop]

2013-01-05T12:27:25Z

Protected "1vim" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:27, 5 January 2013
(No difference)

OCA at 12:27, 5 January 2013

2013-01-05T12:27:22Z

← Older revision		Revision as of 12:27, 5 January 2013
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	~~{{Seed}}~~
	[[Image:1vim.png\|left\|200px]]		[[Image:1vim.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1vim", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_1vim\| PDB=1vim \| SCENE= }}		{{STRUCTURE_1vim\| PDB=1vim \| SCENE= }}

	===Crystal structure of an hypothetical protein===		===Crystal structure of an hypothetical protein===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16021622}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16021622 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16021622}}		{{ABSTRACT_PUBMED_16021622}}

	==About this Structure==		==About this Structure==
	~~1VIM~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA].		[[1vim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16021622~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016021622</ref><references group="xtra"/>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: GenomiX, Structural.]]		[[Category: GenomiX, Structural.]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
			[[Category: Unknown function]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 09:03:44 2009''~~

OCA at 07:03, 18 February 2009

2009-02-18T07:03:46Z

← Older revision		Revision as of 07:03, 18 February 2009
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	==About this Structure==		==About this Structure==
	1VIM is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA].		1VIM is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VIM OCA].

	==Reference==		==Reference==
	Structural analysis of a set of proteins resulting from a bacterial genomics project., Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ, Proteins. 2005 Sep 1;60(4):787-96. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16021622 16021622]~~		<ref group="xtra">PMID:16021622</ref><references group="xtra"/>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	~~[[Category: Single protein]]~~
	[[Category: GenomiX, Structural.]]		[[Category: GenomiX, Structural.]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 15~~:17:~~03 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:03:44 2009''

OCA at 12:17, 29 July 2008

2008-07-29T12:17:06Z

← Older revision		Revision as of 12:17, 29 July 2008
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	[[Image:1vim.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:1vim.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1vim\| PDB=1vim \| SCENE= }}		{{STRUCTURE_1vim\| PDB=1vim \| SCENE= }}

	~~'''~~Crystal structure of an hypothetical protein~~'''~~		===Crystal structure of an hypothetical protein===


	~~==Overview==~~		<!--
	The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this ~~work was 80 structures~~, ~~covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of~~ the ~~remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed~~ to ~~deposit these structures in~~ the ~~Protein Data Bank, along with the associated X-ray diffraction data~~ (~~including refined experimental phases) and experimentally confirmed sequences~~. ~~BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3~~.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the ~~structural coverage of gene space is proceeding rapidly~~. ~~More distant sequence~~-~~structure relationships between the SGX and PDB structures were investigated using PDB~~-~~BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.~~		The line below this paragraph, {{ABSTRACT_PUBMED_16021622}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 16021622 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_16021622}}

	==About this Structure==		==About this Structure==
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	[[Category: GenomiX, Structural.]]		[[Category: GenomiX, Structural.]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 12~~:34:25 2008''
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