7w58 - Revision history

OCA at 17:36, 29 November 2023

OCA — Wed, 29 Nov 2023 17:36:16 GMT

←Older revision		Revision as of 17:36, 29 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7w58]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W58 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7w58]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W58 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.27Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></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=7w58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w58 OCA], [https://pdbe.org/7w58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w58 RCSB], [https://www.ebi.ac.uk/pdbsum/7w58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w58 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=7w58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w58 OCA], [https://pdbe.org/7w58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w58 RCSB], [https://www.ebi.ac.uk/pdbsum/7w58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w58 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A8B4R1L0_MYCSM A0A8B4R1L0_MYCSM]] Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein.[HAMAP-Rule:MF_00101]	+	[https://www.uniprot.org/uniprot/A0A8B4R1L0_MYCSM A0A8B4R1L0_MYCSM] Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein.[HAMAP-Rule:MF_00101]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:33, 8 September 2022

OCA — Thu, 08 Sep 2022 05:33:31 GMT

←Older revision		Revision as of 05:33, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7w58' size='340' side='right'caption='[[7w58]], [[Resolution\|resolution]] 2.27Å' scene=''>		<StructureSection load='7w58' size='340' side='right'caption='[[7w58]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7w58]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W58 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7w58]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W58 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Holo-[acyl-carrier-protein]_synthase Holo-[acyl-carrier-protein] synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.8.7 2.7.8.7] </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=7w58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w58 OCA], [https://pdbe.org/7w58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w58 RCSB], [https://www.ebi.ac.uk/pdbsum/7w58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w58 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=7w58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w58 OCA], [https://pdbe.org/7w58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w58 RCSB], [https://www.ebi.ac.uk/pdbsum/7w58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w58 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A8B4R1L0_MYCSM A0A8B4R1L0_MYCSM]] Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein.[HAMAP-Rule:MF_00101]	+	[[https://www.uniprot.org/uniprot/A0A8B4R1L0_MYCSM A0A8B4R1L0_MYCSM]] Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein.[HAMAP-Rule:MF_00101]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The unintended crystallization of proteins which generally originate from the expression host instead of the target recombinant proteins is periodically reported. Despite the massive technological advances in the field, assigning a structural model to the corresponding diffraction data is not a trivial task. Here, the structure of acyl-carrier protein synthase (AcpS) from Mycobacterium smegmatis (msAcpS), which crystallized inadvertently in an experimental setup to grow crystals of a Mycobacterium tuberculosis protein using M. smegmatis as an expression system, is reported. After numerous unsuccessful attempts to solve the structure of the target protein by the molecular-replacement method no convincing solutions were obtained, indicating that the diffraction data may correspond to a crystal of an artifactual protein, which was finally identified by the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) server. The msAcpS structure was solved at 2.27 A resolution and structural analysis showed an overall conserved fold. msAcpS formed a trimeric structure similar to those of other reported structures of AcpS from various organisms; however, the residues involved in trimer formation are not strictly conserved. An unrelated metal ion (Ni(2+)), which was possibly incorporated during protein purification, was observed in the proximity of His49 and His116. Structural and sequence differences were observed in the loop connecting the alpha3 and alpha4 helices that is responsible for the open and closed conformations of the enzyme. Moreover, the structural analysis of msAcpS augments the current understanding of this enzyme, which plays a crucial role in the functional activation of acyl-carrier proteins in the fatty-acid biosynthesis pathway.	+
-		+
-	Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously.,Bhatia I, Yadav S, Biswal BK Acta Crystallogr F Struct Biol Commun. 2022 Jul 1;78(Pt 7):252-264. doi:, 10.1107/S2053230X22005738. Epub 2022 Jun 15. PMID:35787552<ref>PMID:35787552</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7w58" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bhatia, I~~]]	+	[[Category: Mycolicibacterium smegmatis]]
-	[[Category: ~~Biswal, B K~~]]	+	[[Category: Bhatia I]]
-	[[Category: ~~Yadav, S~~]]	+	[[Category: Biswal BK]]
-	[[Category: ~~Acp]]~~	+	[[Category: Yadav S]]
-	~~[[Category: Mycobacterium smegmati]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:18, 20 July 2022

OCA — Wed, 20 Jul 2022 07:18:17 GMT

←Older revision		Revision as of 07:18, 20 July 2022
Line 1:		Line 1:

-	==~~n/a~~==	+	==Crystal structure of acyl-carrier protein synthase from Mycobacterium smegmatis==
-	<StructureSection load='7w58' size='340' side='right'caption='[[7w58]]' scene=''>	+	<StructureSection load='7w58' size='340' side='right'caption='[[7w58]], [[Resolution\|resolution]] 2.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W58 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7w58]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W58 FirstGlance]. <br>
-	</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=7w58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w58 OCA], [https://pdbe.org/7w58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w58 RCSB], [https://www.ebi.ac.uk/pdbsum/7w58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w58 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Holo-[acyl-carrier-protein]_synthase Holo-[acyl-carrier-protein] synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.8.7 2.7.8.7] </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=7w58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w58 OCA], [https://pdbe.org/7w58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w58 RCSB], [https://www.ebi.ac.uk/pdbsum/7w58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w58 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A8B4R1L0_MYCSM A0A8B4R1L0_MYCSM]] Transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of acyl-carrier-protein.[HAMAP-Rule:MF_00101]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The unintended crystallization of proteins which generally originate from the expression host instead of the target recombinant proteins is periodically reported. Despite the massive technological advances in the field, assigning a structural model to the corresponding diffraction data is not a trivial task. Here, the structure of acyl-carrier protein synthase (AcpS) from Mycobacterium smegmatis (msAcpS), which crystallized inadvertently in an experimental setup to grow crystals of a Mycobacterium tuberculosis protein using M. smegmatis as an expression system, is reported. After numerous unsuccessful attempts to solve the structure of the target protein by the molecular-replacement method no convincing solutions were obtained, indicating that the diffraction data may correspond to a crystal of an artifactual protein, which was finally identified by the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) server. The msAcpS structure was solved at 2.27 A resolution and structural analysis showed an overall conserved fold. msAcpS formed a trimeric structure similar to those of other reported structures of AcpS from various organisms; however, the residues involved in trimer formation are not strictly conserved. An unrelated metal ion (Ni(2+)), which was possibly incorporated during protein purification, was observed in the proximity of His49 and His116. Structural and sequence differences were observed in the loop connecting the alpha3 and alpha4 helices that is responsible for the open and closed conformations of the enzyme. Moreover, the structural analysis of msAcpS augments the current understanding of this enzyme, which plays a crucial role in the functional activation of acyl-carrier proteins in the fatty-acid biosynthesis pathway.
		+
		+	Identification, structure determination and analysis of Mycobacterium smegmatis acyl-carrier protein synthase (AcpS) crystallized serendipitously.,Bhatia I, Yadav S, Biswal BK Acta Crystallogr F Struct Biol Commun. 2022 Jul 1;78(Pt 7):252-264. doi:, 10.1107/S2053230X22005738. Epub 2022 Jun 15. PMID:35787552<ref>PMID:35787552</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7w58" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~N/a~~]]	+	[[Category: Bhatia, I]]
		+	[[Category: Biswal, B K]]
		+	[[Category: Yadav, S]]
		+	[[Category: Acp]]
		+	[[Category: Mycobacterium smegmati]]
		+	[[Category: Transferase]]

OCA at 07:28, 29 June 2022

OCA — Wed, 29 Jun 2022 07:28:28 GMT

←Older revision		Revision as of 07:28, 29 June 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7w58 ~~is ON HOLD until Paper Publication~~	+	==n/a==
-		+	<StructureSection load='7w58' size='340' side='right'caption='[[7w58]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W58 FirstGlance]. <br>
-	~~Description~~:	+	</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=7w58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w58 OCA], [https://pdbe.org/7w58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w58 RCSB], [https://www.ebi.ac.uk/pdbsum/7w58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w58 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: N/a]]

OCA at 15:47, 15 December 2021

OCA — Wed, 15 Dec 2021 15:47:39 GMT

←Older revision		Revision as of 15:47, 15 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7w58 is ON HOLD	+	The entry 7w58 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7w58" [edit=sysop:move=sysop]

OCA — Wed, 08 Dec 2021 08:45:05 GMT

Protected "7w58" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:45, 8 December 2021

OCA: New page: '''Unreleased structure''' The entry 7w58 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Dec 2021 08:45:03 GMT

New page: '''Unreleased structure''' The entry 7w58 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7w58 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]