6m3l - Revision history

OCA at 15:14, 29 November 2023

OCA — Wed, 29 Nov 2023 15:14:23 GMT

←Older revision		Revision as of 15:14, 29 November 2023
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	<StructureSection load='6m3l' size='340' side='right'caption='[[6m3l]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='6m3l' size='340' side='right'caption='[[6m3l]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m3l]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrab Pyrab~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M3L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6M3L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m3l]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5] 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=6M3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M3L FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6l2o\|6l2o]], [[6l2n\|6l2n]]</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]] 2.75Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">PAB0105 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=272844 PYRAB])~~</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=6m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m3l OCA], [https://pdbe.org/6m3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m3l RCSB], [https://www.ebi.ac.uk/pdbsum/6m3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m3l 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=6m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m3l OCA], [~~http~~://pdbe.org/6m3l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m3l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m3l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m3l ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G8ZFZ3_PYRAB G8ZFZ3_PYRAB]
	<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: ~~Pyrab~~]]	+	[[Category: Pyrococcus abyssi GE5]]
-	[[Category: Ito, T]]	+	[[Category: Synthetic construct]]
-	[[Category: Miyazono, K]]	+	[[Category: Ito T]]
-	[[Category: Tanokura, M]]	+	[[Category: Miyazono K]]
-	[[Category: Wang, D]]	+	[[Category: Tanokura M]]
-	~~[[Category: Glycosylase]]~~	+	[[Category: Wang D]]
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 07:13, 15 April 2020

OCA — Wed, 15 Apr 2020 07:13:10 GMT

←Older revision		Revision as of 07:13, 15 April 2020
Line 3:		Line 3:
	<StructureSection load='6m3l' size='340' side='right'caption='[[6m3l]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='6m3l' size='340' side='right'caption='[[6m3l]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m3l]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M3L OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6M3L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m3l]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M3L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M3L FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6l2o\|6l2o]], [[6l2n\|6l2n]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6l2o\|6l2o]], [[6l2n\|6l2n]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAB0105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAB0105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</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=6m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m3l OCA], [http://pdbe.org/6m3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m3l RCSB], [http://www.ebi.ac.uk/pdbsum/6m3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m3l 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=6m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m3l OCA], [http://pdbe.org/6m3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m3l RCSB], [http://www.ebi.ac.uk/pdbsum/6m3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m3l ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	R.PabI is a restriction DNA glycosylase that recognizes the sequence 5'-GTAC-3' and hydrolyses the N-glycosidic bond of adenine in the recognition sequence. R.PabI drastically bends and unwinds the recognition sequence of double-stranded DNA (dsDNA) and flips the adenine and guanine bases in the recognition sequence into the catalytic and recognition sites on the protein surface. In this study, we determined the crystal structure of the R.PabI-dsDNA complex in which the dsDNA is drastically bent by the binding of R.PabI but the base pairs are not unwound. This structure is predicted to be important for the indirect readout of the recognition sequence by R.PabI. In the complex structure, wedge loops of the R.PabI dimer are inserted into the minor groove of dsDNA to stabilize the deformed dsDNA structure. A base stacking is distorted between the two wedge-inserted regions. R.PabI is predicted to utilize the distorted base stacking for the detection of the recognition sequence.
		+
		+	Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.,Miyazono KI, Wang D, Ito T, Tanokura M Nucleic Acids Res. 2020 Mar 31. pii: 5814050. doi: 10.1093/nar/gkaa184. PMID:32232412<ref>PMID:32232412</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6m3l" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:34, 1 April 2020

OCA — Wed, 01 Apr 2020 09:34:39 GMT

←Older revision		Revision as of 09:34, 1 April 2020
Line 3:		Line 3:
	<StructureSection load='6m3l' size='340' side='right'caption='[[6m3l]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='6m3l' size='340' side='right'caption='[[6m3l]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m3l]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M3L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m3l]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M3L FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6l2o\|6l2o]], [[6l2n\|6l2n]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6l2o\|6l2o]], [[6l2n\|6l2n]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAB0105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</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=6m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m3l OCA], [http://pdbe.org/6m3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m3l RCSB], [http://www.ebi.ac.uk/pdbsum/6m3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m3l 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=6m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m3l OCA], [http://pdbe.org/6m3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m3l RCSB], [http://www.ebi.ac.uk/pdbsum/6m3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m3l ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pyrab]]
	[[Category: Ito, T]]		[[Category: Ito, T]]
	[[Category: Miyazono, K]]		[[Category: Miyazono, K]]

OCA at 09:42, 18 March 2020

OCA — Wed, 18 Mar 2020 09:42:04 GMT

←Older revision		Revision as of 09:42, 18 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6m3l is ON HOLD~~	+	==Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex==
-		+	<StructureSection load='6m3l' size='340' side='right'caption='[[6m3l]], [[Resolution\|resolution]] 2.75Å' scene=''>
-	~~Authors: Miyazono, K., Wang, D., Ito, T., Tanokura, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6m3l]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M3L FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6l2o\|6l2o]], [[6l2n\|6l2n]]</td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m3l OCA], [http://pdbe.org/6m3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m3l RCSB], [http://www.ebi.ac.uk/pdbsum/6m3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m3l ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ito, T]]
	[[Category: Miyazono, K]]		[[Category: Miyazono, K]]
		+	[[Category: Tanokura, M]]
	[[Category: Wang, D]]		[[Category: Wang, D]]
-	[[Category: ~~Tanokura, M~~]]	+	[[Category: Glycosylase]]
-	[[Category: ~~Ito, T~~]]	+	[[Category: Hydrolase-dna complex]]

OCA: Protected "6m3l" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 05:59:18 GMT

Protected "6m3l" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:59, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6m3l is ON HOLD Authors: Miyazono, K., Wang, D., Ito, T., Tanokura, M. Description: Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) ...

OCA — Wed, 11 Mar 2020 05:59:16 GMT

New page: '''Unreleased structure''' The entry 6m3l is ON HOLD Authors: Miyazono, K., Wang, D., Ito, T., Tanokura, M. Description: Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) ...

New page

'''Unreleased structure'''

The entry 6m3l is ON HOLD

Authors: Miyazono, K., Wang, D., Ito, T., Tanokura, M.

Description: Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex
[[Category: Unreleased Structures]]
[[Category: Miyazono, K]]
[[Category: Wang, D]]
[[Category: Tanokura, M]]
[[Category: Ito, T]]