1lme - Revision history

OCA at 09:15, 16 August 2023

OCA — Wed, 16 Aug 2023 09:15:47 GMT

←Older revision		Revision as of 09:15, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1lme' size='340' side='right'caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lme' size='340' side='right'caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43589 Atcc 43589~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LME FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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]] 2.2Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1lm4\|1lm4]]~~, [[~~1lm6~~\|~~1lm6~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88]~~ </~~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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [https://pdbe.org/1lme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [https://www.ebi.ac.uk/pdbsum/1lme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lme ProSAT], [https://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [https://pdbe.org/1lme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [https://www.ebi.ac.uk/pdbsum/1lme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lme ProSAT], [https://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DEF_THEMA DEF_THEMA]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).	+	[https://www.uniprot.org/uniprot/DEF_THEMA DEF_THEMA] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Peptide deformylase~~]]	+	[[Category: Thermotoga maritima]]
-	[[Category: Ericson, C]]	+	[[Category: Ericson C]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Klock H]]
-	[[Category: Klock, H]]	+	[[Category: Kreusch A]]
-	[[Category: Kreusch, A]]	+	[[Category: Lee CC]]
-	[[Category: Lee~~, C C~~]]	+	[[Category: Lesley SA]]
-	[[Category: Lesley~~, S A~~]]	+	[[Category: McMullan D]]
-	[[Category: McMullan, D]]	+	[[Category: Ng K]]
-	[[Category: Ng, K]]	+	[[Category: Shin T]]
-	[[Category: Shin, T]]	+	[[Category: Spraggon G]]
-	[[Category: Spraggon, G]]	+	[[Category: Vincent J]]
-	[[Category: Vincent, J]]	+	[[Category: Warner I]]
-	[[Category: Warner, I]]	+
-	~~[[Category: Deformylation]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Jcsg]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Pdf]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Thermophile~~]]	+

OCA at 06:46, 18 August 2021

OCA — Wed, 18 Aug 2021 06:46:41 GMT

←Older revision		Revision as of 06:46, 18 August 2021
Line 3:		Line 3:
	<StructureSection load='1lme' size='340' side='right'caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lme' size='340' side='right'caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LME FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lm4\|1lm4]], [[1lm6\|1lm6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lm4\|1lm4]], [[1lm6\|1lm6]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [~~http~~://pdbe.org/1lme PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lme PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lme ProSAT], [~~http~~://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [https://pdbe.org/1lme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [https://www.ebi.ac.uk/pdbsum/1lme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lme ProSAT], [https://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DEF_THEMA DEF_THEMA]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).	+	[[https://www.uniprot.org/uniprot/DEF_THEMA DEF_THEMA]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:12, 13 November 2019

OCA — Wed, 13 Nov 2019 12:12:15 GMT

←Older revision		Revision as of 12:12, 13 November 2019
Line 1:		Line 1:

	==Crystal Structure of Peptide Deformylase from Thermotoga maritima==		==Crystal Structure of Peptide Deformylase from Thermotoga maritima==
-	<StructureSection load='1lme' size='340' side='right' caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1lme' size='340' side='right'caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LME FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LME FirstGlance]. <br>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43589]]		[[Category: Atcc 43589]]
		+	[[Category: Large Structures]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Ericson, C]]		[[Category: Ericson, C]]

OCA at 07:48, 31 January 2018

OCA — Wed, 31 Jan 2018 07:48:17 GMT

←Older revision		Revision as of 07:48, 31 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Peptide Deformylase from Thermotoga maritima==		==Crystal Structure of Peptide Deformylase from Thermotoga maritima==
	<StructureSection load='1lme' size='340' side='right' caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lme' size='340' side='right' caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lm4\|1lm4]], [[1lm6\|1lm6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lm4\|1lm4]], [[1lm6\|1lm6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [http://pdbe.org/1lme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [http://www.ebi.ac.uk/pdbsum/1lme PDBsum], [http://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [http://pdbe.org/1lme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [http://www.ebi.ac.uk/pdbsum/1lme PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lme ProSAT], [http://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lm/1lme_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lm/1lme_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 02:15, 7 February 2016

OCA — Sun, 07 Feb 2016 02:15:06 GMT

←Older revision		Revision as of 02:15, 7 February 2016
Line 18:		Line 18:
	<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=1lme ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:42, 9 September 2015

OCA — Wed, 09 Sep 2015 20:42:46 GMT

←Older revision		Revision as of 20:42, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1lme' size='340' side='right' caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lme' size='340' side='right' caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermotoga_maritima Thermotoga maritima~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LME FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lm4\|1lm4]], [[1lm6\|1lm6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lm4\|1lm4]], [[1lm6\|1lm6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [http://www.ebi.ac.uk/pdbsum/1lme PDBsum], [http://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [http://pdbe.org/1lme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [http://www.ebi.ac.uk/pdbsum/1lme PDBsum], [http://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1lme" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43589]]
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
-	[[Category: Thermotoga maritima]]
	[[Category: Ericson, C]]		[[Category: Ericson, C]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 07:00, 24 December 2014

OCA — Wed, 24 Dec 2014 07:00:05 GMT

←Older revision		Revision as of 07:00, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LME FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LME FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</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=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lm4\|1lm4]], [[1lm6\|1lm6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lm4\|1lm4]], [[1lm6\|1lm6]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [http://www.ebi.ac.uk/pdbsum/1lme PDBsum], [http://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [http://www.ebi.ac.uk/pdbsum/1lme PDBsum], [http://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DEF_THEMA DEF_THEMA]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
-	[[Category: Ericson, C.]]	+	[[Category: Ericson, C]]
-	[[Category: ~~JCSG, Joint Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Klock, H.]]	+	[[Category: Klock, H]]
-	[[Category: Kreusch, A.]]	+	[[Category: Kreusch, A]]
-	[[Category: Lee, C C.]]	+	[[Category: Lee, C C]]
-	[[Category: Lesley, S A.]]	+	[[Category: Lesley, S A]]
-	[[Category: McMullan, D.]]	+	[[Category: McMullan, D]]
-	[[Category: Ng, K.]]	+	[[Category: Ng, K]]
-	[[Category: Shin, T.]]	+	[[Category: Shin, T]]
-	[[Category: Spraggon, G.]]	+	[[Category: Spraggon, G]]
-	[[Category: Vincent, J.]]	+	[[Category: Vincent, J]]
-	[[Category: Warner, I.]]	+	[[Category: Warner, I]]
	[[Category: Deformylation]]		[[Category: Deformylation]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Jcsg]]		[[Category: Jcsg]]
-	[[Category: Joint center for structural genomic]]
	[[Category: Metalloenzyme]]		[[Category: Metalloenzyme]]
	[[Category: Pdf]]		[[Category: Pdf]]
-	[[Category: ~~Peptide deformylase]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
-	~~[[Category: Psi]]~~	+
-	~~[[Category: Structural genomic~~]]	+
	[[Category: Thermophile]]		[[Category: Thermophile]]

OCA at 13:10, 28 September 2014

OCA — Sun, 28 Sep 2014 13:10:41 GMT

←Older revision		Revision as of 13:10, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lme.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Peptide Deformylase from Thermotoga maritima==
		+	<StructureSection load='1lme' size='340' side='right' caption='[[1lme]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LME FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lm4\|1lm4]], [[1lm6\|1lm6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=1lme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lme RCSB], [http://www.ebi.ac.uk/pdbsum/1lme PDBsum], [http://www.topsan.org/Proteins/JCSG/1lme TOPSAN]</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/lm/1lme_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 ==
		+	Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four members of this enzyme family, two from the Gram-positive pathogens Streptococcus pneumoniae and Staphylococcus aureus, and two from the Gram-negative bacteria Thermotoga maritima and Pseudomonas aeruginosa. Combined with the known structures from the Escherichia coli enzyme and the recently solved structure of the eukaryotic deformylase from Plasmodium falciparum, a complete picture of the peptide deformylase structure and function relationship is emerging. This understanding could help guide a more rational design of inhibitors. A structure-based comparison between PDFs reveals some conserved differences between type I and type II enzymes. Moreover, our structures provide insights into the known instability of PDF caused by oxidation of the metal-ligating cysteine residue.

-	~~{{STRUCTURE_1lme\| PDB=1lme \| SCENE= }}~~	+	Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase.,Kreusch A, Spraggon G, Lee CC, Klock H, McMullan D, Ng K, Shin T, Vincent J, Warner I, Ericson C, Lesley SA J Mol Biol. 2003 Jul 4;330(2):309-21. PMID:12823970<ref>PMID:12823970</ref>

-	~~===Crystal Structure~~ of ~~Peptide Deformylase from Thermotoga maritima===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12823970}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1lme]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermotoga_maritima Thermotoga maritima]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012823970<~~/~~ref~~><~~ref group="xtra">PMID:016049914</ref><references group="xtra"~~/>	+
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]

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

OCA — Wed, 05 Dec 2012 19:48:46 GMT

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

←Older revision

Revision as of 19:48, 5 December 2012

OCA at 19:48, 5 December 2012

OCA — Wed, 05 Dec 2012 19:48:43 GMT

←Older revision		Revision as of 19:48, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1lme.png\|left\|200px]]		[[Image:1lme.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lme", 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_1lme\| PDB=1lme \| SCENE= }}		{{STRUCTURE_1lme\| PDB=1lme \| SCENE= }}

	===Crystal Structure of Peptide Deformylase from Thermotoga maritima===		===Crystal Structure of Peptide Deformylase from Thermotoga maritima===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12823970}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12823970 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12823970}}		{{ABSTRACT_PUBMED_12823970}}

	==About this Structure==		==About this Structure==
-	~~1LME~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA].	+	[[1lme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LME OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12823970~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012823970</ref><ref group="xtra">PMID:016049914</ref><references group="xtra"/>
	[[Category: Peptide deformylase]]		[[Category: Peptide deformylase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
Line 39:		Line 27:
	[[Category: Warner, I.]]		[[Category: Warner, I.]]
	[[Category: Deformylation]]		[[Category: Deformylation]]
		+	[[Category: Hydrolase]]
	[[Category: Jcsg]]		[[Category: Jcsg]]
	[[Category: Joint center for structural genomic]]		[[Category: Joint center for structural genomic]]
Line 48:		Line 37:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Thermophile]]		[[Category: Thermophile]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 10:13:37 2009''