7cd4 - Revision history

OCA at 08:38, 17 October 2024

2024-10-17T08:38:23Z

← Older revision		Revision as of 08:38, 17 October 2024
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	<StructureSection load='7cd4' size='340' side='right'caption='[[7cd4]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='7cd4' size='340' side='right'caption='[[7cd4]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7cd4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._natto_BEST195 Bacillus subtilis subsp. natto BEST195].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CD4 FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CD4 FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</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]] 2.1Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7cd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd4 OCA], [https://pdbe.org/7cd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd4 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd4 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=7cd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd4 OCA], [https://pdbe.org/7cd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd4 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd4 ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	~~[https://www.uniprot.org/uniprot/D4G3D4_BACNB D4G3D4_BACNB]~~
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Bacillus subtilis subsp. natto BEST195]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fujimoto Z]]		[[Category: Fujimoto Z]]
	[[Category: Kimura K]]		[[Category: Kimura K]]
	[[Category: Kishine N]]		[[Category: Kishine N]]

OCA at 16:05, 29 November 2023

2023-11-29T16:05:09Z

← Older revision		Revision as of 16:05, 29 November 2023
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	==Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.==		==Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.==
	<StructureSection load='7cd4' size='340' side='right'caption='[[7cd4]]' scene=''>		<StructureSection load='7cd4' size='340' side='right'caption='[[7cd4]], [[Resolution\|resolution]] 2.10Å' 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=7CD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CD4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7cd4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._natto_BEST195 Bacillus subtilis subsp. natto BEST195]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CD4 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=7cd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd4 OCA], [https://pdbe.org/7cd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd4 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd4 ProSAT]</span></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]] 2.1Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7cd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd4 OCA], [https://pdbe.org/7cd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd4 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd4 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/D4G3D4_BACNB D4G3D4_BACNB]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Bacillus subtilis YabJ protein belongs to the highly conserved YjgF/YER057c/UK114 family, which has a homotrimeric quaternary structure. The dominant allele of yabJ gene that is caused by a single amino acid mutation of Ser103Phe enables poly-gamma-glutamic acid (gammaPGA) production of B. subtilis under conditions where the cell-density signal transduction was disturbed by the loss of DegQ function. X-ray crystallography of recombinant proteins revealed that unlike the homotrimeric wild-type YabJ, the mutant YabJ(Ser103Phe) had a homotetrameric quaternary structure, and the structural change appeared to be triggered by an inversion of the fifth beta-strand. The YabJ homotetramer has a hole that is highly accessible, penetrating through the tetramer, and 2 surface concaves as potential ligand-binding sites. Western blot analyses revealed that the conformational change was also induced in vivo by the Ser103Phe mutation.

			Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family.,Fujimoto Z, Hong LTT, Kishine N, Suzuki N, Kimura K Biosci Biotechnol Biochem. 2021 Feb 18;85(2):297-306. doi: 10.1093/bbb/zbaa037. PMID:33590041<ref>PMID:33590041</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7cd4" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacillus subtilis subsp. natto BEST195]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fujimoto Z]]		[[Category: Fujimoto Z]]
	[[Category: Kimura K]]		[[Category: Kimura K]]
	[[Category: Kishine N]]		[[Category: Kishine N]]

OCA at 14:45, 3 March 2021

2021-03-03T14:45:16Z

← Older revision		Revision as of 14:45, 3 March 2021
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	~~'''Unreleased structure'''~~

	~~The entry 7cd4 is ON HOLD until Paper Publication~~		==Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.==
			<StructureSection load='7cd4' size='340' side='right'caption='[[7cd4]]' scene=''>
	~~Authors: Fujimoto, Z., Kishine, N., Kimura, K.~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CD4 FirstGlance]. <br>
	~~Description:~~ Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.		</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=7cd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cd4 OCA], [https://pdbe.org/7cd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cd4 RCSB], [https://www.ebi.ac.uk/pdbsum/7cd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cd4 ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Kimura, K~~]]		__TOC__
	[[Category: ~~Kishine, N~~]]		</StructureSection>
	[[Category: ~~Fujimoto, Z~~]]		[[Category: Large Structures]]
			[[Category: Fujimoto Z]]
			[[Category: Kimura K]]
			[[Category: Kishine N]]

OCA at 04:07, 5 August 2020

2020-08-05T04:07:18Z

← Older revision		Revision as of 04:07, 5 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7cd4 is ON HOLD		The entry 7cd4 is ON HOLD until Paper Publication

	Authors: Fujimoto, Z., Kishine, N., Kimura, K.		Authors: Fujimoto, Z., Kishine, N., Kimura, K.
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	Description: Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.		Description: Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Kimura, K]]
	[[Category: Kishine, N]]		[[Category: Kishine, N]]
	[[Category: Fujimoto, Z]]		[[Category: Fujimoto, Z]]
	~~[[Category: Kimura, K]]~~

OCA: Protected "7cd4" [edit=sysop:move=sysop]

2020-06-24T18:56:03Z

Protected "7cd4" [edit=sysop:move=sysop]

← Older revision	Revision as of 18:56, 24 June 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7cd4 is ON HOLD Authors: Fujimoto, Z., Kishine, N., Kimura, K. Description: Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ...

2020-06-24T18:56:00Z

New page: '''Unreleased structure''' The entry 7cd4 is ON HOLD Authors: Fujimoto, Z., Kishine, N., Kimura, K. Description: Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ...

New page

'''Unreleased structure'''

The entry 7cd4 is ON HOLD

Authors: Fujimoto, Z., Kishine, N., Kimura, K.

Description: Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein.
[[Category: Unreleased Structures]]
[[Category: Kishine, N]]
[[Category: Fujimoto, Z]]
[[Category: Kimura, K]]