5h8v - Revision history

OCA at 07:27, 9 August 2023

OCA — Wed, 09 Aug 2023 07:27:33 GMT

←Older revision		Revision as of 07:27, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='5h8v' size='340' side='right'caption='[[5h8v]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5h8v' size='340' side='right'caption='[[5h8v]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h8v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Maize Maize~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H8V FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</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">[[3b2f\|3b2f]]~~, [[~~5h8y~~\|~~5h8y]], [[5h92\|5h92~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=4577 MAIZE])</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=5h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8v OCA], [https://pdbe.org/5h8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h8v RCSB], [https://www.ebi.ac.uk/pdbsum/5h8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8v 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/Assimilatory_sulfite_reductase_(ferredoxin) Assimilatory sulfite reductase (ferredoxin)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.7.1 1.8.7.1] </~~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=5h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8v OCA], [~~http~~://pdbe.org/5h8v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h8v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h8v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SIR_MAIZE SIR_MAIZE]] Essential protein with sulfite reductase activity required in assimilatory sulfate reduction pathway during both primary and secondary metabolism and thus involved in development and growth.<ref>PMID:10712553</ref> <ref>PMID:11163356</ref> <ref>PMID:14871491</ref> <ref>PMID:17371503</ref> DNA-binding protein that binds to both double-stranded and single-stranded DNA without significant sequence specificity to reversibly repress the transcriptional activity of chloroplast nucleoids by promoting DNA compaction and possibly regulate DNA replication.<ref>PMID:11163356</ref>	+	[https://www.uniprot.org/uniprot/SIR_MAIZE SIR_MAIZE] Essential protein with sulfite reductase activity required in assimilatory sulfate reduction pathway during both primary and secondary metabolism and thus involved in development and growth.<ref>PMID:10712553</ref> <ref>PMID:11163356</ref> <ref>PMID:14871491</ref> <ref>PMID:17371503</ref> DNA-binding protein that binds to both double-stranded and single-stranded DNA without significant sequence specificity to reversibly repress the transcriptional activity of chloroplast nucleoids by promoting DNA compaction and possibly regulate DNA replication.<ref>PMID:11163356</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Maize~~]]	+	[[Category: Zea mays]]
-	[[Category: Hase, T]]	+	[[Category: Hase T]]
-	[[Category: Kurisu, G]]	+	[[Category: Kurisu G]]
-	[[Category: Nakayama, M]]	+	[[Category: Nakayama M]]
-	~~[[Category: Ferredoxin]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Sulfite reductase~~]]	+

OCA at 07:15, 19 February 2020

OCA — Wed, 19 Feb 2020 07:15:26 GMT

←Older revision		Revision as of 07:15, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of the complex between maize Sulfite Reductase and ferredoxin in the form-1 crystal==		==Crystal structure of the complex between maize Sulfite Reductase and ferredoxin in the form-1 crystal==
-	<StructureSection load='5h8v' size='340' side='right' caption='[[5h8v]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5h8v' size='340' side='right'caption='[[5h8v]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h8v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h8v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Maize Maize]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H8V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2f\|3b2f]], [[5h8y\|5h8y]], [[5h92\|5h92]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2f\|3b2f]], [[5h8y\|5h8y]], [[5h92\|5h92]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4577 MAIZE])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Assimilatory_sulfite_reductase_(ferredoxin) Assimilatory sulfite reductase (ferredoxin)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.7.1 1.8.7.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Assimilatory_sulfite_reductase_(ferredoxin) Assimilatory sulfite reductase (ferredoxin)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.7.1 1.8.7.1] </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=5h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8v OCA], [http://pdbe.org/5h8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h8v RCSB], [http://www.ebi.ac.uk/pdbsum/5h8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8v 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=5h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8v OCA], [http://pdbe.org/5h8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h8v RCSB], [http://www.ebi.ac.uk/pdbsum/5h8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8v ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Maize]]
	[[Category: Hase, T]]		[[Category: Hase, T]]
	[[Category: Kurisu, G]]		[[Category: Kurisu, G]]

OCA at 08:03, 10 August 2016

OCA — Wed, 10 Aug 2016 08:03:34 GMT

←Older revision		Revision as of 08:03, 10 August 2016
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2f\|3b2f]], [[5h8y\|5h8y]], [[5h92\|5h92]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2f\|3b2f]], [[5h8y\|5h8y]], [[5h92\|5h92]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Assimilatory_sulfite_reductase_(ferredoxin) Assimilatory sulfite reductase (ferredoxin)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.7.1 1.8.7.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Assimilatory_sulfite_reductase_(ferredoxin) Assimilatory sulfite reductase (ferredoxin)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.7.1 1.8.7.1] </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=5h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8v OCA], [http://pdbe.org/5h8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h8v RCSB], [http://www.ebi.ac.uk/pdbsum/5h8v 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=5h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8v OCA], [http://pdbe.org/5h8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h8v RCSB], [http://www.ebi.ac.uk/pdbsum/5h8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 11:27, 12 May 2016

OCA — Thu, 12 May 2016 11:27:56 GMT

←Older revision		Revision as of 11:27, 12 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5h8v is ~~ON HOLD~~	+	==Crystal structure of the complex between maize Sulfite Reductase and ferredoxin in the form-1 crystal==
		+	<StructureSection load='5h8v' size='340' side='right' caption='[[5h8v]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5h8v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H8V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SRM:SIROHEME'>SRM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3b2f\|3b2f]], [[5h8y\|5h8y]], [[5h92\|5h92]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Assimilatory_sulfite_reductase_(ferredoxin) Assimilatory sulfite reductase (ferredoxin)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.7.1 1.8.7.1] </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=5h8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8v OCA], [http://pdbe.org/5h8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h8v RCSB], [http://www.ebi.ac.uk/pdbsum/5h8v PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SIR_MAIZE SIR_MAIZE]] Essential protein with sulfite reductase activity required in assimilatory sulfate reduction pathway during both primary and secondary metabolism and thus involved in development and growth.<ref>PMID:10712553</ref> <ref>PMID:11163356</ref> <ref>PMID:14871491</ref> <ref>PMID:17371503</ref> DNA-binding protein that binds to both double-stranded and single-stranded DNA without significant sequence specificity to reversibly repress the transcriptional activity of chloroplast nucleoids by promoting DNA compaction and possibly regulate DNA replication.<ref>PMID:11163356</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The structure of the complex of maize sulfite reductase (SiR) and ferredoxin (Fd) has been determined by X-ray crystallography. Co-crystals of the two proteins prepared under different conditions were subjected to the diffraction analysis and three possible structures of the complex were solved. Although topological relationship of SiR and Fd varied in each of the structures, two characteristics common to all structures were found in the pattern of protein-protein interactions and positional arrangements of redox centres; (i) a few negative residues of Fd contact with a narrow area of SiR with positive electrostatic surface potential and (ii) [2Fe-2S] cluster of Fd and [4Fe-4S] cluster of SiR are in a close proximity with the shortest distance around 12 A. Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. These combined results suggest that the productive electron transfer complex of SiR and Fd could be formed through multiple processes of the electrostatic intermolecular interaction and this implication is discussed in terms of the multi-functionality of Fd in various redox metabolisms.

-	~~Authors: Kurisu, G~~., ~~Nakayama~~, M., ~~Hase~~, T.	+	Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin.,Kim JY, Nakayama M, Toyota H, Kurisu G, Hase T J Biochem. 2016 Feb 26. pii: mvw016. PMID:26920048<ref>PMID:26920048</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5h8v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hase, T]]
	[[Category: Kurisu, G]]		[[Category: Kurisu, G]]
	[[Category: Nakayama, M]]		[[Category: Nakayama, M]]
-	[[Category: ~~Hase, T~~]]	+	[[Category: Ferredoxin]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Sulfite reductase]]

OCA: Protected "5h8v" [edit=sysop:move=sysop]

OCA — Wed, 30 Dec 2015 18:24:49 GMT

Protected "5h8v" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:24, 30 December 2015

OCA: New page: '''Unreleased structure''' The entry 5h8v is ON HOLD Authors: Kurisu, G., Nakayama, M., Hase, T. Description: Category: Unreleased Structures Category: Kurisu, G [[Category: N...

OCA — Wed, 30 Dec 2015 18:24:48 GMT

New page: '''Unreleased structure''' The entry 5h8v is ON HOLD Authors: Kurisu, G., Nakayama, M., Hase, T. Description: Category: Unreleased Structures Category: Kurisu, G [[Category: N...

New page

'''Unreleased structure'''

The entry 5h8v is ON HOLD

Authors: Kurisu, G., Nakayama, M., Hase, T.

Description:
[[Category: Unreleased Structures]]
[[Category: Kurisu, G]]
[[Category: Nakayama, M]]
[[Category: Hase, T]]