5h1a - Revision history

OCA at 09:14, 20 March 2024

2024-03-20T09:14:38Z

←Older revision		Revision as of 09:14, 20 March 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5h1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1a OCA], [https://pdbe.org/5h1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h1a RCSB], [https://www.ebi.ac.uk/pdbsum/5h1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1a 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=5h1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1a OCA], [https://pdbe.org/5h1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h1a RCSB], [https://www.ebi.ac.uk/pdbsum/5h1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1a ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix-turn-helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) from Microbacterium sp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments were performed in combination with molecular replacement. CRANK2 from the CCP4 suite successfully phased and modelled the complete structure of a homotetramer composed of 1000 residues in an asymmetric unit, and the model was refined to 2.1 A resolution. The overall structure of Mi-IclR shared the same domain combination as other known IclR structures, but the relative geometry between the DBD and SBD differs. Accordingly, the geometry of the Mi-IclR tetramer was unique: the putative substrate-binding site in each subunit is accessible from the outside of the tetramer, as opposed to buried inside as in the previously known IclR structures. These differences in the domain geometry may contribute to the transcriptional regulation of IclRs.
-
-	Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2.,Akiyama T, Yamada Y, Takaya N, Ito S, Sasaki Y, Yajima S Acta Crystallogr F Struct Biol Commun. 2017 Jan 1;73(Pt 1):16-23. doi:, 10.1107/S2053230X16019208. Epub 2017 Jan 1. PMID:28045389<ref>PMID:28045389</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5h1a" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:48, 2 August 2023

2023-08-02T11:48:50Z

←Older revision		Revision as of 11:48, 2 August 2023
Line 3:		Line 3:
	<StructureSection load='5h1a' size='340' side='right'caption='[[5h1a]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5h1a' size='340' side='right'caption='[[5h1a]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h1a]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aureobacterium_sp~~. ~~Aureobacterium~~ sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H1A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h1a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Microbacterium_sp. Microbacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H1A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.1Å</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=5h1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1a OCA], [~~http~~://pdbe.org/5h1a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h1a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h1a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1a ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5h1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1a OCA], [https://pdbe.org/5h1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h1a RCSB], [https://www.ebi.ac.uk/pdbsum/5h1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1a ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aureobacterium sp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Akiyama, T]]	+	[[Category: Microbacterium sp]]
-	[[Category: Ito, S]]	+	[[Category: Akiyama T]]
-	[[Category: Sasaki, Y]]	+	[[Category: Ito S]]
-	[[Category: Takaya, N]]	+	[[Category: Sasaki Y]]
-	[[Category: Yajima, S]]	+	[[Category: Takaya N]]
-	[[Category: Yamada, Y]]	+	[[Category: Yajima S]]
-	~~[[Category: Dna-binding]]~~	+	[[Category: Yamada Y]]
-	~~[[Category: Transcription regulator~~]]	+

OCA at 10:11, 26 February 2020

2020-02-26T10:11:19Z

←Older revision		Revision as of 10:11, 26 February 2020
Line 1:		Line 1:

	==Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2==		==Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2==
-	<StructureSection load='5h1a' size='340' side='right' caption='[[5h1a]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5h1a' size='340' side='right'caption='[[5h1a]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h1a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H1A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h1a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aureobacterium_sp. Aureobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H1A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5h1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1a OCA], [http://pdbe.org/5h1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h1a RCSB], [http://www.ebi.ac.uk/pdbsum/5h1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1a ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5h1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1a OCA], [http://pdbe.org/5h1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h1a RCSB], [http://www.ebi.ac.uk/pdbsum/5h1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1a ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aureobacterium sp]]
		+	[[Category: Large Structures]]
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]
	[[Category: Ito, S]]		[[Category: Ito, S]]

OCA at 16:21, 18 January 2017

2017-01-18T16:21:57Z

←Older revision		Revision as of 16:21, 18 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5h1a is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2==
		+	<StructureSection load='5h1a' size='340' side='right' caption='[[5h1a]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5h1a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H1A FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5h1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h1a OCA], [http://pdbe.org/5h1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h1a RCSB], [http://www.ebi.ac.uk/pdbsum/5h1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h1a ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix-turn-helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) from Microbacterium sp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments were performed in combination with molecular replacement. CRANK2 from the CCP4 suite successfully phased and modelled the complete structure of a homotetramer composed of 1000 residues in an asymmetric unit, and the model was refined to 2.1 A resolution. The overall structure of Mi-IclR shared the same domain combination as other known IclR structures, but the relative geometry between the DBD and SBD differs. Accordingly, the geometry of the Mi-IclR tetramer was unique: the putative substrate-binding site in each subunit is accessible from the outside of the tetramer, as opposed to buried inside as in the previously known IclR structures. These differences in the domain geometry may contribute to the transcriptional regulation of IclRs.

-	~~Authors: Akiyama~~, T., Yamada, Y., Takaya, N., Ito, S., Sasaki, Y., Yajima, S.	+	Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2.,Akiyama T, Yamada Y, Takaya N, Ito S, Sasaki Y, Yajima S Acta Crystallogr F Struct Biol Commun. 2017 Jan 1;73(Pt 1):16-23. doi:, 10.1107/S2053230X16019208. Epub 2017 Jan 1. PMID:28045389<ref>PMID:28045389</ref>

-	~~Description: Crystal structure~~ of ~~an IclR homolog from Microbacterium sp~~. ~~strain HM58-2~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Yajima, S]]~~	+	<div class="pdbe-citations 5h1a" style="background-color:#fffaf0;"></div>
-	~~[[Category: Takaya, N]]~~	+	== References ==
-	~~[[Category: Sasaki, Y]]~~	+	<references/>
-	~~[[Category: Ito, S]]~~	+	__TOC__
		+	</StructureSection>
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]
		+	[[Category: Ito, S]]
		+	[[Category: Sasaki, Y]]
		+	[[Category: Takaya, N]]
		+	[[Category: Yajima, S]]
	[[Category: Yamada, Y]]		[[Category: Yamada, Y]]
		+	[[Category: Dna-binding]]
		+	[[Category: Transcription regulator]]

OCA at 13:38, 9 December 2016

2016-12-09T13:38:04Z

←Older revision		Revision as of 13:38, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h1a is ON HOLD	+	The entry 5h1a is ON HOLD until Paper Publication

	Authors: Akiyama, T., Yamada, Y., Takaya, N., Ito, S., Sasaki, Y., Yajima, S.		Authors: Akiyama, T., Yamada, Y., Takaya, N., Ito, S., Sasaki, Y., Yajima, S.

OCA at 13:12, 26 October 2016

2016-10-26T13:12:41Z

←Older revision		Revision as of 13:12, 26 October 2016
Line 5:		Line 5:
	Authors: Akiyama, T., Yamada, Y., Takaya, N., Ito, S., Sasaki, Y., Yajima, S.		Authors: Akiyama, T., Yamada, Y., Takaya, N., Ito, S., Sasaki, Y., Yajima, S.

-	Description: Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2.	+	Description: Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yajima, S]]		[[Category: Yajima, S]]

OCA: Protected "5h1a" [edit=sysop:move=sysop]

2016-10-19T12:01:50Z

Protected "5h1a" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:01, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5h1a is ON HOLD Authors: Akiyama, T., Yamada, Y., Takaya, N., Ito, S., Sasaki, Y., Yajima, S. Description: Crystal structure of an IclR homolog fro...

2016-10-19T12:01:48Z

New page: '''Unreleased structure''' The entry 5h1a is ON HOLD Authors: Akiyama, T., Yamada, Y., Takaya, N., Ito, S., Sasaki, Y., Yajima, S. Description: Crystal structure of an IclR homolog fro...

New page

'''Unreleased structure'''

The entry 5h1a is ON HOLD

Authors: Akiyama, T., Yamada, Y., Takaya, N., Ito, S., Sasaki, Y., Yajima, S.

Description: Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2.
[[Category: Unreleased Structures]]
[[Category: Yajima, S]]
[[Category: Takaya, N]]
[[Category: Sasaki, Y]]
[[Category: Ito, S]]
[[Category: Akiyama, T]]
[[Category: Yamada, Y]]