3lnl - Revision history

OCA at 10:21, 21 February 2024

OCA — Wed, 21 Feb 2024 10:21:21 GMT

←Older revision		Revision as of 10:21, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3lnl' size='340' side='right'caption='[[3lnl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3lnl' size='340' side='right'caption='[[3lnl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lnl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Staan Staan~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LNL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lnl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_N315 Staphylococcus aureus subsp. aureus N315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LNL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nyd\|2nyd]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1388 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158879 STAAN])~~</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=3lnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lnl OCA], [https://pdbe.org/3lnl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lnl RCSB], [https://www.ebi.ac.uk/pdbsum/3lnl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lnl 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=3lnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lnl OCA], [https://pdbe.org/3lnl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lnl RCSB], [https://www.ebi.ac.uk/pdbsum/3lnl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lnl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GCH1L_STAAN GCH1L_STAAN]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=3lnl 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=3lnl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function. RESULTS: The structure of SA1388 has been solved to 2.0A resolution by single wavelength anomalous dispersion phasing method using selenium anomalous signals. It reveals a canonical NIF3-like fold containing two domains with a PII-like domain inserted in the middle of the polypeptide. The N and C terminal halves of the NIF3-like domains are involved in dimerization, while the PII domain forms trimeric contacts with symmetry related monomers. Overall, the NIF3-like domains of SA1388 are organized as a hexameric toroid similar to its homologs, E. coli ybgI and the hypothetical protein SP1609 from Streptococcus pneumoniae. The openings on either side of the toroid are partially covered by trimeric "lids" formed by the PII domains. The junction of the two NIF3 domains has two zinc ions bound at what appears to be a histidine rich active site. A well-defined electron density corresponding to an endogenously bound ligand of unknown identity is observed in close proximity to the metal site. CONCLUSION: SA1388 is the third member of the NIF3-like family of proteins to be structurally characterized, the other two also being hypothetical proteins of unknown function. The structure of SA1388 confirms our earlier prediction that the inserted domain that separates the two NIF3 domains adopts a PII-like fold and reveals an overall capped toroidal arrangement for the protein hexamer. The six PII-like domains form two trimeric "lids" that cap the central cavity of the toroid on either side and provide only small openings to allow regulated entry of small molecules into the occluded chamber. The presence of the electron density of the bound ligand may provide important clues on the likely function of NIF3-like proteins.
-
-	Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center.,Saikatendu KS, Zhang X, Kinch L, Leybourne M, Grishin NV, Zhang H BMC Struct Biol. 2006 Dec 23;6:27. PMID:17187687<ref>PMID:17187687</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3lnl" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Staan~~]]	+	[[Category: Staphylococcus aureus subsp. aureus N315]]
-	[[Category: Chruszcz, M]]	+	[[Category: Chruszcz M]]
-	[[Category: Minor, W]]	+	[[Category: Minor W]]
-	[[Category: Singh~~, K S~~]]	+	[[Category: Singh KS]]
-	[[Category: Zhang, H]]	+	[[Category: Zhang H]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang X]]
-	~~[[Category: Protein sa1388]]~~	+
-	~~[[Category: Selenomethionine sad]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 12:36, 13 October 2021

OCA — Wed, 13 Oct 2021 12:36:51 GMT

←Older revision		Revision as of 12:36, 13 October 2021
Line 1:		Line 1:

	==Crystal structure of Staphylococcus aureus protein SA1388==		==Crystal structure of Staphylococcus aureus protein SA1388==
-	<StructureSection load='3lnl' size='340' side='right' caption='[[3lnl]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3lnl' size='340' side='right'caption='[[3lnl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lnl]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Staan Staan]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3LNL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lnl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staan Staan]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LNL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</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=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</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">[[2nyd\|2nyd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nyd\|2nyd]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1388 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158879 STAAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1388 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158879 STAAN])</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=3lnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lnl OCA], [~~http~~://pdbe.org/3lnl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3lnl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3lnl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3lnl 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=3lnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lnl OCA], [https://pdbe.org/3lnl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lnl RCSB], [https://www.ebi.ac.uk/pdbsum/3lnl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lnl ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ln/3lnl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ln/3lnl_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>
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Staan]]		[[Category: Staan]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]

OCA at 12:33, 4 August 2016

OCA — Thu, 04 Aug 2016 12:33:16 GMT

←Older revision		Revision as of 12:33, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Staphylococcus aureus protein SA1388==		==Crystal structure of Staphylococcus aureus protein SA1388==
	<StructureSection load='3lnl' size='340' side='right' caption='[[3lnl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3lnl' size='340' side='right' caption='[[3lnl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lnl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus_subsp._aureus_n315 Staphylococcus aureus subsp. aureus n315~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LNL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lnl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staan Staan]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LNL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</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=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</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">[[2nyd\|2nyd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nyd\|2nyd]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1388 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158879 ~~Staphylococcus aureus subsp. aureus N315~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1388 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158879 STAAN])</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=3lnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lnl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lnl RCSB], [http://www.ebi.ac.uk/pdbsum/3lnl 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=3lnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lnl OCA], [http://pdbe.org/3lnl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lnl RCSB], [http://www.ebi.ac.uk/pdbsum/3lnl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lnl ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=3lnl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	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 3lnl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staphylococcus aureus subsp. aureus n315~~]]	+	[[Category: Staan]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]
	[[Category: Minor, W]]		[[Category: Minor, W]]

OCA at 15:06, 18 December 2014

OCA — Thu, 18 Dec 2014 15:06:40 GMT

←Older revision		Revision as of 15:06, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3lnl\| PDB~~=3lnl \| ~~SCENE~~= }}	+	==Crystal structure of Staphylococcus aureus protein SA1388==
-	===~~Crystal~~ structure of Staphylococcus aureus ~~protein~~ SA1388===	+	<StructureSection load='3lnl' size='340' side='right' caption='[[3lnl]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_17187687}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3lnl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_n315 Staphylococcus aureus subsp. aureus n315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LNL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</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">[[2nyd\|2nyd]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SA1388 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=158879 Staphylococcus aureus subsp. aureus N315])</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=3lnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lnl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lnl RCSB], [http://www.ebi.ac.uk/pdbsum/3lnl 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/ln/3lnl_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 ==
		+	BACKGROUND: The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function. RESULTS: The structure of SA1388 has been solved to 2.0A resolution by single wavelength anomalous dispersion phasing method using selenium anomalous signals. It reveals a canonical NIF3-like fold containing two domains with a PII-like domain inserted in the middle of the polypeptide. The N and C terminal halves of the NIF3-like domains are involved in dimerization, while the PII domain forms trimeric contacts with symmetry related monomers. Overall, the NIF3-like domains of SA1388 are organized as a hexameric toroid similar to its homologs, E. coli ybgI and the hypothetical protein SP1609 from Streptococcus pneumoniae. The openings on either side of the toroid are partially covered by trimeric "lids" formed by the PII domains. The junction of the two NIF3 domains has two zinc ions bound at what appears to be a histidine rich active site. A well-defined electron density corresponding to an endogenously bound ligand of unknown identity is observed in close proximity to the metal site. CONCLUSION: SA1388 is the third member of the NIF3-like family of proteins to be structurally characterized, the other two also being hypothetical proteins of unknown function. The structure of SA1388 confirms our earlier prediction that the inserted domain that separates the two NIF3 domains adopts a PII-like fold and reveals an overall capped toroidal arrangement for the protein hexamer. The six PII-like domains form two trimeric "lids" that cap the central cavity of the toroid on either side and provide only small openings to allow regulated entry of small molecules into the occluded chamber. The presence of the electron density of the bound ligand may provide important clues on the likely function of NIF3-like proteins.

-	~~==About this~~ Structure==	+	Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center.,Saikatendu KS, Zhang X, Kinch L, Leybourne M, Grishin NV, Zhang H BMC Struct Biol. 2006 Dec 23;6:27. PMID:17187687<ref>PMID:17187687</ref>
-	~~[[3lnl]] is~~ a ~~2 chain structure with sequence~~ from ~~[http://en~~.~~wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_n315 Staphylococcus~~ aureus ~~subsp~~. ~~aureus n315]~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann.ac.il~~/~~oca-bin/ocashort?id=3LNL OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:017187687</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Staphylococcus aureus subsp. aureus n315]]		[[Category: Staphylococcus aureus subsp. aureus n315]]
-	[[Category: Chruszcz, M.]]	+	[[Category: Chruszcz, M]]
-	[[Category: Minor, W.]]	+	[[Category: Minor, W]]
-	[[Category: Singh, K S.]]	+	[[Category: Singh, K S]]
-	[[Category: Zhang, H.]]	+	[[Category: Zhang, H]]
-	[[Category: Zhang, X.]]	+	[[Category: Zhang, X]]
	[[Category: Protein sa1388]]		[[Category: Protein sa1388]]
	[[Category: Selenomethionine sad]]		[[Category: Selenomethionine sad]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA: Protected "3lnl" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2013 23:28:10 GMT

Protected "3lnl" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:28, 10 April 2013

OCA at 23:28, 10 April 2013

OCA — Wed, 10 Apr 2013 23:28:07 GMT

←Older revision		Revision as of 23:28, 10 April 2013
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-	{{Seed}}
-	[[Image:3lnl.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3lnl", 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_3lnl\| PDB=3lnl \| SCENE= }}		{{STRUCTURE_3lnl\| PDB=3lnl \| SCENE= }}
-
	===Crystal structure of Staphylococcus aureus protein SA1388===		===Crystal structure of Staphylococcus aureus protein SA1388===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17187687}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17187687 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17187687}}		{{ABSTRACT_PUBMED_17187687}}

	==About this Structure==		==About this Structure==
-	~~3LNL~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp.~~_aureus~~ Staphylococcus aureus subsp. aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA].	+	[[3lnl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_n315 Staphylococcus aureus subsp. aureus n315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17187687~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017187687</ref><references group="xtra"/><references/>
-	[[Category: Staphylococcus aureus subsp. aureus]]	+	[[Category: Staphylococcus aureus subsp. aureus n315]]
	[[Category: Chruszcz, M.]]		[[Category: Chruszcz, M.]]
	[[Category: Minor, W.]]		[[Category: Minor, W.]]
Line 33:		Line 17:
	[[Category: Selenomethionine sad]]		[[Category: Selenomethionine sad]]
	[[Category: Unknown function]]		[[Category: Unknown function]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 17 09:30:12 2010''

OCA at 07:30, 17 March 2010

OCA — Wed, 17 Mar 2010 07:30:13 GMT

←Older revision		Revision as of 07:30, 17 March 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3lnl.jpg\|left\|200px]]

-	The ~~entry 3lnl~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3lnl", 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_3lnl\| PDB=3lnl \| SCENE= }}

-	~~Authors: Singh, K.S., Chruszcz, M., Zhang, X., Minor, W., Zhang, H.~~	+	===Crystal structure of Staphylococcus aureus protein SA1388===

-	Description: Crystal structure of Staphylococcus aureus protein SA1388

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar ~~10 13~~:13:22 2010''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_17187687}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17187687 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17187687}}
		+
		+	==About this Structure==
		+	3LNL is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus Staphylococcus aureus subsp. aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LNL OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:17187687</ref><references group="xtra"/>
		+	[[Category: Staphylococcus aureus subsp. aureus]]
		+	[[Category: Chruszcz, M.]]
		+	[[Category: Minor, W.]]
		+	[[Category: Singh, K S.]]
		+	[[Category: Zhang, H.]]
		+	[[Category: Zhang, X.]]
		+	[[Category: Protein sa1388]]
		+	[[Category: Selenomethionine sad]]
		+	[[Category: Unknown function]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 17 09:30:12 2010''

OCA at 11:13, 10 March 2010

OCA — Wed, 10 Mar 2010 11:13:22 GMT

←Older revision		Revision as of 11:13, 10 March 2010
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	Authors: Singh, K.S., Chruszcz, M., Zhang, X., Minor, W., Zhang, H.		Authors: Singh, K.S., Chruszcz, M., Zhang, X., Minor, W., Zhang, H.

-	Description: ~~CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN~~ SA1388	+	Description: Crystal structure of Staphylococcus aureus protein SA1388

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb~~ 10 17:00:06 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 10 13:13:22 2010''

OCA: New page: '''Unreleased structure''' The entry 3lnl is ON HOLD Authors: Singh, K.S., Chruszcz, M., Zhang, X., Minor, W., Zhang, H. Description: CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN...

OCA — Wed, 10 Feb 2010 15:00:07 GMT

New page: '''Unreleased structure''' The entry 3lnl is ON HOLD Authors: Singh, K.S., Chruszcz, M., Zhang, X., Minor, W., Zhang, H. Description: CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN...

New page

'''Unreleased structure'''

The entry 3lnl is ON HOLD

Authors: Singh, K.S., Chruszcz, M., Zhang, X., Minor, W., Zhang, H.

Description: CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS PROTEIN SA1388

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 17:00:06 2010''