1xp4 - Revision history

OCA at 08:07, 25 October 2023

OCA — Wed, 25 Oct 2023 08:07:27 GMT

←Older revision		Revision as of 08:07, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1xp4' size='340' side='right'caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xp4' size='340' side='right'caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strr6 Strr6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.8Å</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=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [https://pdbe.org/1xp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [https://www.ebi.ac.uk/pdbsum/1xp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xp4 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </~~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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [~~http~~://pdbe.org/1xp4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xp4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xp4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8DQ99_STRR6 Q8DQ99_STRR6]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Serine-type D-Ala-D-Ala carboxypeptidase~~]]	+	[[Category: Streptococcus pneumoniae R6]]
-	[[Category: ~~Strr6~~]]	+	[[Category: Dessen A]]
-	[[Category: ~~Dessen, A~~]]	+	[[Category: Di Guilmi AM]]
-	[[Category: Dideberg, O]]	+	[[Category: Dideberg O]]
-	[[Category: Gouellec, A ~~Le]]~~	+	[[Category: Le Gouellec A]]
-	~~[[Category: Guilmi, A M.Di~~]]	+	[[Category: Morlot C]]
-	[[Category: Morlot, C]]	+	[[Category: Pernot L]]
-	[[Category: Pernot, L]]	+	[[Category: Vernet T]]
-	[[Category: Vernet, T]]	+
-	~~[[Category: Five-stranded antiparallel beta-sheet]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Omega-like loop~~]]	+

OCA at 10:12, 6 January 2021

OCA — Wed, 06 Jan 2021 10:12:30 GMT

←Older revision		Revision as of 10:12, 6 January 2021
Line 1:		Line 1:

	==Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae==		==Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae==
-	<StructureSection load='1xp4' size='340' side='right' caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1xp4' size='340' side='right'caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://pdbe.org/1xp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xp4 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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://pdbe.org/1xp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xp4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Strr6]]		[[Category: Strr6]]

OCA at 07:38, 18 April 2018

OCA — Wed, 18 Apr 2018 07:38:09 GMT

←Older revision		Revision as of 07:38, 18 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae==		==Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae==
	<StructureSection load='1xp4' size='340' side='right' caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xp4' size='340' side='right' caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://pdbe.org/1xp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://pdbe.org/1xp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xp4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xp/1xp4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xp/1xp4_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>

OCA at 05:34, 10 February 2016

OCA — Wed, 10 Feb 2016 05:34:55 GMT

←Older revision		Revision as of 05:34, 10 February 2016
Line 17:		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=1xp4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:52, 11 September 2015

OCA — Fri, 11 Sep 2015 05:52:18 GMT

←Older revision		Revision as of 05:52, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1xp4' size='340' side='right' caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xp4' size='340' side='right' caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptococcus_pneumoniae_r6 Streptococcus pneumoniae r6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 ~~Streptococcus pneumoniae R6~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://pdbe.org/1xp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		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 1xp4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: ~~Streptococcus pneumoniae r6~~]]	+	[[Category: Strr6]]
	[[Category: Dessen, A]]		[[Category: Dessen, A]]
	[[Category: Dideberg, O]]		[[Category: Dideberg, O]]

OCA at 10:44, 8 January 2015

OCA — Thu, 08 Jan 2015 10:44:07 GMT

←Older revision		Revision as of 10:44, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_r6 Streptococcus pneumoniae r6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_r6 Streptococcus pneumoniae r6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><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>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 Streptococcus pneumoniae R6])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 Streptococcus pneumoniae R6])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 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 33:		Line 33:
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Streptococcus pneumoniae r6]]		[[Category: Streptococcus pneumoniae r6]]
-	[[Category: Dessen, A.]]	+	[[Category: Dessen, A]]
-	[[Category: Dideberg, O.]]	+	[[Category: Dideberg, O]]
-	[[Category: Gouellec, A Le.]]	+	[[Category: Gouellec, A Le]]
-	[[Category: Guilmi, A M.Di.]]	+	[[Category: Guilmi, A M.Di]]
-	[[Category: Morlot, C.]]	+	[[Category: Morlot, C]]
-	[[Category: Pernot, L.]]	+	[[Category: Pernot, L]]
-	[[Category: Vernet, T.]]	+	[[Category: Vernet, T]]
	[[Category: Five-stranded antiparallel beta-sheet]]		[[Category: Five-stranded antiparallel beta-sheet]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Omega-like loop]]		[[Category: Omega-like loop]]

OCA at 20:41, 28 September 2014

OCA — Sun, 28 Sep 2014 20:41:09 GMT

←Older revision		Revision as of 20:41, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xp4.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae==
		+	<StructureSection load='1xp4' size='340' side='right' caption='[[1xp4]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_r6 Streptococcus pneumoniae r6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XP4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 Streptococcus pneumoniae R6])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 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/xp/1xp4_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 ==
		+	Penicillin-binding proteins (PBPs) are membrane-associated enzymes which perform critical functions in the bacterial cell division process. The single d-Ala,d-Ala (d,d)-carboxypeptidase in Streptococcus pneumoniae, PBP3, has been shown to play a key role in control of availability of the peptidoglycal substrate during cell growth. Here, we have biochemically characterized and solved the crystal structure of a soluble form of PBP3 to 2.8 A resolution. PBP3 folds into an NH(2)-terminal, d,d-carboxypeptidase-like domain, and a COOH-terminal, elongated beta-rich region. The carboxypeptidase domain harbors the classic signature of the penicilloyl serine transferase superfamily, in that it contains a central, five-stranded antiparallel beta-sheet surrounded by alpha-helices. As in other carboxypeptidases, which are present in species whose peptidoglycan stem peptide has a lysine residue at the third position, PBP3 has a 14-residue insertion at the level of its omega loop, a feature that distinguishes it from carboxypeptidases from bacteria whose peptidoglycan harbors a diaminopimelate moiety at this position. PBP3 performs substrate acylation in a highly efficient manner (k(cat)/K(m) = 50,500 M(-1) x s(-1)), an event that may be linked to role in control of pneumococcal peptidoglycan reticulation. A model that places PBP3 poised vertically on the bacterial membrane suggests that its COOH-terminal region could act as a pedestal, placing the active site in proximity to the peptidoglycan and allowing the protein to "skid" on the surface of the membrane, trimming pentapeptides during the cell growth and division processes.

-	~~{{STRUCTURE_1xp4\| PDB=1xp4 \| SCENE= }}~~	+	Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae.,Morlot C, Pernot L, Le Gouellec A, Di Guilmi AM, Vernet T, Dideberg O, Dessen A J Biol Chem. 2005 Apr 22;280(16):15984-91. Epub 2004 Dec 13. PMID:15596446<ref>PMID:15596446</ref>

-	~~===Crystal structure~~ of ~~a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15596446}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xp4]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptococcus_pneumoniae_r6 Streptococcus pneumoniae r6]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA].~~	+	</StructureSection>
-		+
-	==~~See Also==~~	+
-	*[[Carboxypeptidase\|Carboxypeptidase]]	+
-		+
-	~~==Reference~~==	+
-	<~~ref group="xtra">PMID:015596446<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Streptococcus pneumoniae r6]]		[[Category: Streptococcus pneumoniae r6]]

OCA at 16:30, 20 October 2012

OCA — Sat, 20 Oct 2012 16:30:12 GMT

←Older revision		Revision as of 16:30, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1xp4]] is a 4 chain structure ~~of [[Carboxypeptidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_r6 Streptococcus pneumoniae r6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA].	+	[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_r6 Streptococcus pneumoniae r6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA].

	==See Also==		==See Also==

OCA: Protected "1xp4" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 21:54:06 GMT

Protected "1xp4" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:54, 26 July 2012

OCA at 21:54, 26 July 2012

OCA — Thu, 26 Jul 2012 21:54:05 GMT

←Older revision		Revision as of 21:54, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xp4.png\|left\|200px]]		[[Image:1xp4.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xp4", 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_1xp4\| PDB=1xp4 \| SCENE= }}		{{STRUCTURE_1xp4\| PDB=1xp4 \| SCENE= }}

	===Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae===		===Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15596446}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15596446 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15596446}}		{{ABSTRACT_PUBMED_15596446}}

	==About this Structure==		==About this Structure==
-	~~1XP4~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/~~Streptococcus_pneumoniae~~ Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA].	+	[[1xp4]] is a 4 chain structure of [[Carboxypeptidase]] with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_r6 Streptococcus pneumoniae r6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA].
		+
		+	==See Also==
		+	*[[Carboxypeptidase\|Carboxypeptidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15596446~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015596446</ref><references group="xtra"/>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Streptococcus pneumoniae]]	+	[[Category: Streptococcus pneumoniae r6]]
	[[Category: Dessen, A.]]		[[Category: Dessen, A.]]
	[[Category: Dideberg, O.]]		[[Category: Dideberg, O.]]
Line 34:		Line 25:
	[[Category: Vernet, T.]]		[[Category: Vernet, T.]]
	[[Category: Five-stranded antiparallel beta-sheet]]		[[Category: Five-stranded antiparallel beta-sheet]]
		+	[[Category: Hydrolase]]
	[[Category: Omega-like loop]]		[[Category: Omega-like loop]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:49:33 2009''