5f55 - Revision history

OCA at 08:47, 12 July 2023

2023-07-12T08:47:04Z

←Older revision		Revision as of 08:47, 12 July 2023
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	<StructureSection load='5f55' size='340' side='right'caption='[[5f55]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5f55' size='340' side='right'caption='[[5f55]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f55]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus~~ radiodurans~~" raj et al~~. ~~1960~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F55 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5F55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f55]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F55 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5f54\|5f54]], [[5f56\|5f56]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">recJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])~~</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=5f55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f55 OCA], [https://pdbe.org/5f55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f55 RCSB], [https://www.ebi.ac.uk/pdbsum/5f55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f55 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5f55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f55 OCA], [~~http~~://pdbe.org/5f55 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f55 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f55 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f55 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D0EM60_DEIRD D0EM60_DEIRD]
	<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: ~~Micrococcus~~ radiodurans ~~raj et al. 1960~~]]	+	[[Category: Deinococcus radiodurans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cheng, K~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Hua, Y~~]]	+	[[Category: Cheng K]]
-	[[Category: ~~Zhao,~~ Y]]	+	[[Category: Hua Y]]
-	[[Category: ~~Dna binding protein-dna complex]]~~	+	[[Category: Zhao Y]]
-	~~[[Category: Dna end resection]]~~	+
-	~~[[Category: Recf pathway]]~~	+
-	~~[[Category: Single-strand-dna]]~~	+
-	~~[[Category: Two-metal-ion catalysis~~]]	+

OCA at 07:59, 29 April 2020

2020-04-29T07:59:56Z

←Older revision		Revision as of 07:59, 29 April 2020
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	==Structure of RecJ complexed with DNA==		==Structure of RecJ complexed with DNA==
-	<StructureSection load='5f55' size='340' side='right' caption='[[5f55]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5f55' size='340' side='right'caption='[[5f55]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f55]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F55 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f55]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F55 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5F55 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f54\|5f54]], [[5f56\|5f56]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f54\|5f54]], [[5f56\|5f56]]</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=5f55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f55 OCA], [http://pdbe.org/5f55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f55 RCSB], [http://www.ebi.ac.uk/pdbsum/5f55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f55 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">recJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5f55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f55 OCA], [http://pdbe.org/5f55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f55 RCSB], [http://www.ebi.ac.uk/pdbsum/5f55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f55 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5f55" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5f55" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Micrococcus radiodurans raj et al. 1960]]
		+	[[Category: Large Structures]]
	[[Category: Cheng, K]]		[[Category: Cheng, K]]
	[[Category: Hua, Y]]		[[Category: Hua, Y]]

OCA at 04:34, 9 September 2016

2016-09-09T04:34:53Z

←Older revision		Revision as of 04:34, 9 September 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f54\|5f54]], [[5f56\|5f56]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f54\|5f54]], [[5f56\|5f56]]</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=5f55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f55 OCA], [http://pdbe.org/5f55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f55 RCSB], [http://www.ebi.ac.uk/pdbsum/5f55 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=5f55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f55 OCA], [http://pdbe.org/5f55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f55 RCSB], [http://www.ebi.ac.uk/pdbsum/5f55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f55 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:08, 20 June 2016

2016-06-20T15:08:40Z

←Older revision		Revision as of 15:08, 20 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5f55 is ~~ON HOLD until Paper~~ Publication	+	==Structure of RecJ complexed with DNA==
		+	<StructureSection load='5f55' size='340' side='right' caption='[[5f55]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5f55]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F55 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5f54\|5f54]], [[5f56\|5f56]]</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=5f55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f55 OCA], [http://pdbe.org/5f55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f55 RCSB], [http://www.ebi.ac.uk/pdbsum/5f55 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The resection of DNA strand with a 5 end at double-strand breaks is an essential step in recombinational DNA repair. RecJ, a member of DHH family proteins, is the only 5 nuclease involved in the RecF recombination pathway. Here, we report the crystal structures of Deinococcus radiodurans RecJ in complex with deoxythymidine monophosphate (dTMP), ssDNA, the C-terminal region of single-stranded DNA-binding protein (SSB-Ct) and a mechanistic insight into the RecF pathway. A terminal 5 -phosphate-binding pocket above the active site determines the 5 -3 polarity of the deoxy-exonuclease of RecJ; a helical gateway at the entrance to the active site admits ssDNA only; and the continuous stacking interactions between protein and nine nucleotides ensure the processive end resection. The active site of RecJ in the N-terminal domain contains two divalent cations that coordinate the nucleophilic water. The ssDNA makes a 180 degrees turn at the scissile phosphate. The C-terminal domain of RecJ binds the SSB-Ct, which explains how RecJ and SSB work together to efficiently process broken DNA ends for homologous recombination.

-	~~Authors~~:	+	Structural basis for DNA 5 -end resection by RecJ.,Cheng K, Xu H, Chen X, Wang L, Tian B, Zhao Y, Hua Y Elife. 2016 Apr 8;5. pii: e14294. doi: 10.7554/eLife.14294. PMID:27058167<ref>PMID:27058167</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5f55" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cheng, K]]
		+	[[Category: Hua, Y]]
		+	[[Category: Zhao, Y]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna end resection]]
		+	[[Category: Recf pathway]]
		+	[[Category: Single-strand-dna]]
		+	[[Category: Two-metal-ion catalysis]]

OCA at 12:47, 15 May 2016

2016-05-15T12:47:28Z

←Older revision		Revision as of 12:47, 15 May 2016
Line 3:		Line 3:
	The entry 5f55 is ON HOLD until Paper Publication		The entry 5f55 is ON HOLD until Paper Publication

-	Authors: ~~Hua, Y., Zhao, Y., Cheng, K.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Zhao, Y]]
-	[[Category: Cheng, K]]
-	[[Category: Hua, Y]]

OCA at 11:12, 23 December 2015

2015-12-23T11:12:21Z

←Older revision		Revision as of 11:12, 23 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f55 is ON HOLD	+	The entry 5f55 is ON HOLD until Paper Publication

	Authors: Hua, Y., Zhao, Y., Cheng, K.		Authors: Hua, Y., Zhao, Y., Cheng, K.

OCA: Protected "5f55" [edit=sysop:move=sysop]

2015-12-09T12:39:05Z

Protected "5f55" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:39, 9 December 2015

OCA: New page: '''Unreleased structure''' The entry 5f55 is ON HOLD Authors: Hua, Y., Zhao, Y., Cheng, K. Description: Category: Unreleased Structures Category: Zhao, Y [[Category: Cheng, K]...

2015-12-09T12:39:03Z

New page: '''Unreleased structure''' The entry 5f55 is ON HOLD Authors: Hua, Y., Zhao, Y., Cheng, K. Description: Category: Unreleased Structures Category: Zhao, Y [[Category: Cheng, K]...

New page

'''Unreleased structure'''

The entry 5f55 is ON HOLD

Authors: Hua, Y., Zhao, Y., Cheng, K.

Description:
[[Category: Unreleased Structures]]
[[Category: Zhao, Y]]
[[Category: Cheng, K]]
[[Category: Hua, Y]]