3kw3 - Revision history

OCA at 08:25, 6 September 2023

OCA — Wed, 06 Sep 2023 08:25:47 GMT

←Older revision		Revision as of 08:25, 6 September 2023
Line 1:		Line 1:

	==Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate==		==Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate==
-	<StructureSection load='3kw3' size='340' side='right' caption='[[3kw3]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='3kw3' size='340' side='right'caption='[[3kw3]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_49882 Atcc 49882~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KW3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KW3 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=LLP:(2S)-2-AMINO-6~~-[[~~3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL~~]~~METHYLIDENEAMINO~~]~~HEXANOIC+ACID'>LLP</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]] 2.04Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>alr, BH12810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=38323 ATCC 49882])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number~~ [~~http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~5~~.1.1.1 5.1.1.1~~] </~~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=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [https://pdbe.org/3kw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [https://www.ebi.ac.uk/pdbsum/3kw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kw3 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=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [~~http~~://pdbe.org/3kw3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kw3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kw3 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~Q6G2F2_BARHE Q6G2F2_BARHE]~~] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids ~~(By similarity)~~.[HAMAP-Rule:MF_01201]	+	[https://www.uniprot.org/uniprot/A0A0H3LZE4_BARHE A0A0H3LZE4_BARHE] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.[HAMAP-Rule:MF_01201]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/3kw3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/3kw3_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 31:

	==See Also==		==See Also==
-	*[[Alanine racemase\|Alanine racemase]]	+	*[[Alanine racemase 3D structures\|Alanine racemase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alanine racemase~~]]	+	[[Category: Bartonella henselae]]
-	[[Category: ~~Atcc 49882]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Cat-scratch disease]]~~	+
-	~~[[Category: Iodide soak]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Llp]]~~	+
-	~~[[Category: Niaid]]~~	+
-	~~[[Category: Ssgcid~~]]	+

OCA at 22:56, 5 August 2016

OCA — Fri, 05 Aug 2016 22:56:25 GMT

←Older revision		Revision as of 22:56, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate==		==Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate==
	<StructureSection load='3kw3' size='340' side='right' caption='[[3kw3]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='3kw3' size='340' side='right' caption='[[3kw3]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bartonella_henselae Bartonella henselae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KW3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_49882 Atcc 49882]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KW3 FirstGlance]. <br>
-	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-~~LYSINE(~~3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-~~YLMETHANE)~~'>LLP</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr, BH12810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38323 ~~Bartonella henselae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr, BH12810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38323 ATCC 49882])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [http://www.ebi.ac.uk/pdbsum/3kw3 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=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [http://pdbe.org/3kw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [http://www.ebi.ac.uk/pdbsum/3kw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kw3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<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=3kw3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	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 3kw3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
-	[[Category: ~~Bartonella henselae~~]]	+	[[Category: Atcc 49882]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Cat-scratch disease]]		[[Category: Cat-scratch disease]]

OCA at 22:39, 25 December 2014

OCA — Thu, 25 Dec 2014 22:39:29 GMT

←Older revision		Revision as of 22:39, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KW3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KW3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr, BH12810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38323 Bartonella henselae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr, BH12810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38323 Bartonella henselae])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></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=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [http://www.ebi.ac.uk/pdbsum/3kw3 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=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [http://www.ebi.ac.uk/pdbsum/3kw3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q6G2F2_BARHE Q6G2F2_BARHE]] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids (By similarity).[HAMAP-Rule:MF_01201]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 24:		Line 26:
	SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836<ref>PMID:21359836</ref>		SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836<ref>PMID:21359836</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
		+
		+	==See Also==
		+	*[[Alanine racemase\|Alanine racemase]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 37:
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Bartonella henselae]]		[[Category: Bartonella henselae]]
-	[[Category: ~~SSGCID, Seattle~~ Structural ~~Genomics Center for Infectious Disease.]]~~	+	[[Category: Structural genomic]]
-	~~[[Category: Alanine racemase~~]]	+
	[[Category: Cat-scratch disease]]		[[Category: Cat-scratch disease]]
	[[Category: Iodide soak]]		[[Category: Iodide soak]]
Line 39:		Line 43:
	[[Category: Llp]]		[[Category: Llp]]
	[[Category: Niaid]]		[[Category: Niaid]]
-	[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]

OCA at 09:39, 21 May 2014

OCA — Wed, 21 May 2014 09:39:19 GMT

←Older revision		Revision as of 09:39, 21 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3kw3.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate==
		+	<StructureSection load='3kw3' size='340' side='right' caption='[[3kw3]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3kw3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KW3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr, BH12810 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38323 Bartonella henselae])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></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=3kw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kw3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kw3 RCSB], [http://www.ebi.ac.uk/pdbsum/3kw3 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/kw/3kw3_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 Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.

-	<!--	+	SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836<ref>PMID:21359836</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3kw3"~~, ~~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_3kw3\| PDB=3kw3 \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21359836}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21359836 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21359836}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3kw3]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021359836<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Bartonella henselae]]		[[Category: Bartonella henselae]]

OCA: Protected "3kw3" [edit=sysop:move=sysop]

OCA — Wed, 20 Jul 2011 05:23:27 GMT

Protected "3kw3" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:23, 20 July 2011

OCA at 05:23, 20 July 2011

OCA — Wed, 20 Jul 2011 05:23:25 GMT

←Older revision		Revision as of 05:23, 20 July 2011
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3kw3.png\|left\|200px]]
-	[[Image:3kw3.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 12:		Line 11:
	===Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate===		===Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21359836}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21359836 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21359836}}

	==About this Structure==		==About this Structure==
-	~~3KW3~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA].	+	[[3kw3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021359836</ref><references group="xtra"/>
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Bartonella henselae]]		[[Category: Bartonella henselae]]
Line 21:		Line 29:
	[[Category: Cat-scratch disease]]		[[Category: Cat-scratch disease]]
	[[Category: Iodide soak]]		[[Category: Iodide soak]]
		+	[[Category: Isomerase]]
	[[Category: Llp]]		[[Category: Llp]]
	[[Category: Niaid]]		[[Category: Niaid]]
	[[Category: Seattle structural genomics center for infectious disease]]		[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 23 10:26:45 2009''

OCA at 08:26, 23 December 2009

OCA — Wed, 23 Dec 2009 08:26:46 GMT

←Older revision		Revision as of 08:26, 23 December 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3kw3.jpg\|left\|200px]]

-	The ~~entry 3kw3~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3kw3", 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_3kw3\| PDB=3kw3 \| SCENE= }}

-	~~Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	===Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate===

-	Description: Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec ~~9 14~~:45:19 2009''	+	==About this Structure==
		+	3KW3 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bartonella_henselae Bartonella henselae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KW3 OCA].
		+	[[Category: Alanine racemase]]
		+	[[Category: Bartonella henselae]]
		+	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
		+	[[Category: Alanine racemase]]
		+	[[Category: Cat-scratch disease]]
		+	[[Category: Iodide soak]]
		+	[[Category: Llp]]
		+	[[Category: Niaid]]
		+	[[Category: Seattle structural genomics center for infectious disease]]
		+	[[Category: Ssgcid]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 23 10:26:45 2009''

OCA: New page: '''Unreleased structure''' The entry 3kw3 is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of alanine racemase from...

OCA — Wed, 09 Dec 2009 12:45:20 GMT

New page: '''Unreleased structure''' The entry 3kw3 is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of alanine racemase from...

New page

'''Unreleased structure'''

The entry 3kw3 is ON HOLD

Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Description: Crystal structure of alanine racemase from Bartonella henselae with covalently bound pyridoxal phosphate

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 9 14:45:19 2009''