6hlk - Revision history

OCA at 06:15, 7 August 2019

OCA — Wed, 07 Aug 2019 06:15:24 GMT

←Older revision		Revision as of 06:15, 7 August 2019
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	<StructureSection load='6hlk' size='340' side='right'caption='[[6hlk]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='6hlk' size='340' side='right'caption='[[6hlk]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hlk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HLK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hlk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HLK FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CXXR01000010.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6hlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hlk OCA], [http://pdbe.org/6hlk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hlk RCSB], [http://www.ebi.ac.uk/pdbsum/6hlk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hlk 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=6hlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hlk OCA], [http://pdbe.org/6hlk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hlk RCSB], [http://www.ebi.ac.uk/pdbsum/6hlk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hlk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~phenix.refine is~~ a ~~program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range~~ of ~~upper resolution limits using a large repertoire of model parameterizations~~. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the ~~model in a single refinement run. An intuitive graphical user interface is available to guide novice users~~ and to ~~assist advanced users in managing refinement projects~~. X-~~ray or neutron diffraction data can be used separately or jointly in refinement~~. ~~phenix~~.~~refine~~ is ~~tightly integrated into~~ the ~~PHENIX suite, where it serves as a critical component in automated model building~~, ~~final structure refinement~~, ~~structure validation and deposition~~ to the ~~wwPDB~~. ~~This paper presents an overview of~~ the ~~major phenix.refine features~~, ~~with extensive literature references for readers interested~~ in ~~more detailed discussions~~ of the ~~methods~~.	+	Phage-inducible chromosomal islands (PICIs) represent a novel and universal class of mobile genetic elements, which have broad impact on bacterial virulence. In spite of their relevance, how the Gram-negative PICIs hijack the phage machinery for their own specific packaging and how they block phage reproduction remains to be determined. Using genetic and structural analyses, we solve the mystery here by showing that the Gram-negative PICIs encode a protein that simultaneously performs these processes. This protein, which we have named Rpp (for redirecting phage packaging), interacts with the phage terminase small subunit, forming a heterocomplex. This complex is unable to recognize the phage DNA, blocking phage packaging, but specifically binds to the PICI genome, promoting PICI packaging. Our studies reveal the mechanism of action that allows PICI dissemination in nature, introducing a new paradigm in the understanding of the biology of pathogenicity islands and therefore of bacterial pathogen evolution.

-	~~Towards automated crystallographic structure refinement with phenix~~.~~refine.,Afonine PV~~, ~~Grosse~~-~~Kunstleve RW~~, ~~Echols N~~, ~~Headd JJ~~, ~~Moriarty NW~~, ~~Mustyakimov M~~, ~~Terwilliger TC~~, ~~Urzhumtsev A~~, ~~Zwart PH~~, ~~Adams PD Acta Crystallogr D Biol Crystallogr~~. ~~2012 Apr;68~~(~~Pt 4~~)~~:352~~-67. doi:, 10.~~1107~~/~~S0907444912001308~~. ~~Epub 2012 Mar 16~~. PMID:~~22505256~~<ref>PMID:~~22505256~~</ref>	+	Hijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit.,Fillol-Salom A, Bacarizo J, Alqasmi M, Ciges-Tomas JR, Martinez-Rubio R, Roszak AW, Cogdell RJ, Chen J, Marina A, Penades JR Mol Cell. 2019 Jul 8. pii: S1097-2765(19)30473-3. doi:, 10.1016/j.molcel.2019.06.017. PMID:31350119<ref>PMID:31350119</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Alqasmi, M]]		[[Category: Alqasmi, M]]

OCA at 06:15, 31 July 2019

OCA — Wed, 31 Jul 2019 06:15:21 GMT

←Older revision		Revision as of 06:15, 31 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6hlk is ~~ON HOLD until Paper~~ Publication	+	==Hijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit.==
		+	<StructureSection load='6hlk' size='340' side='right'caption='[[6hlk]], [[Resolution\|resolution]] 2.42Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6hlk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HLK FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=6hlk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hlk OCA], [http://pdbe.org/6hlk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hlk RCSB], [http://www.ebi.ac.uk/pdbsum/6hlk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hlk ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

-	~~Authors~~:	+	Towards automated crystallographic structure refinement with phenix.refine.,Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi:, 10.1107/S0907444912001308. Epub 2012 Mar 16. PMID:22505256<ref>PMID:22505256</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6hlk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Alqasmi, M]]
		+	[[Category: Bacarizo, J]]
		+	[[Category: Ciges-Tomas, J R]]
		+	[[Category: Fillol-Salom, A]]
		+	[[Category: Marina, A]]
		+	[[Category: Penades, J R]]
		+	[[Category: Roszak, A W]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Homo-dimer]]
		+	[[Category: Phage interference]]
		+	[[Category: Redirecting packaging protein]]

OCA: Protected "6hlk" [edit=sysop:move=sysop]

OCA — Wed, 19 Sep 2018 18:11:30 GMT

Protected "6hlk" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:11, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6hlk is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Sep 2018 18:11:28 GMT

New page: '''Unreleased structure''' The entry 6hlk is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6hlk is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]