5hnh - Revision history

OCA at 10:47, 16 August 2023

OCA — Wed, 16 Aug 2023 10:47:58 GMT

←Older revision		Revision as of 10:47, 16 August 2023
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	<StructureSection load='5hnh' size='340' side='right'caption='[[5hnh]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='5hnh' size='340' side='right'caption='[[5hnh]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hnh]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_7061 Atcc 7061~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HNH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5HNH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hnh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_pumilus Bacillus pumilus] 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=5HNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HNH FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=YPE:4~~-[~~8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL~~]~~BUT-3-YN-~~1~~-YL+DIHYDROGEN+PHOSPHATE'>YPE</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]] 1.876Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~bpuJIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1408 ATCC 7061~~])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YPE:4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YL+DIHYDROGEN+PHOSPHATE'>YPE</scene></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=5hnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hnh OCA], [~~http~~://pdbe.org/5hnh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hnh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hnh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hnh 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=5hnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hnh OCA], [https://pdbe.org/5hnh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hnh RCSB], [https://www.ebi.ac.uk/pdbsum/5hnh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hnh ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A3FMN7_BACPU A3FMN7_BACPU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 7061~~]]	+	[[Category: Bacillus pumilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aeschimann, W]]	+	[[Category: Synthetic construct]]
-	[[Category: Chau, T T.H]]	+	[[Category: Aeschimann W]]
-	[[Category: Haener, R]]	+	[[Category: Chau T-T-H]]
-	[[Category: Langenegger~~, S M~~]]	+	[[Category: Haener R]]
-	[[Category: Probst, M]]	+	[[Category: Langenegger SM]]
-	[[Category: Stocker, A]]	+	[[Category: Probst M]]
-	~~[[Category: Dna]]~~	+	[[Category: Stocker A]]
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phenanthrene]]~~	+
-	~~[[Category: Pyrene~~]]	+

OCA at 08:24, 27 May 2020

OCA — Wed, 27 May 2020 08:24:55 GMT

←Older revision		Revision as of 08:24, 27 May 2020
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	==Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain==		==Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain==
-	<StructureSection load='5hnh' size='340' side='right' caption='[[5hnh]], [[Resolution\|resolution]] 1.88Å' scene=''>	+	<StructureSection load='5hnh' size='340' side='right'caption='[[5hnh]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hnh]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HNH OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HNH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hnh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_7061 Atcc 7061]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HNH OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HNH FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YPE:4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YL+DIHYDROGEN+PHOSPHATE'>YPE</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=YPE:4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YL+DIHYDROGEN+PHOSPHATE'>YPE</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=5hnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hnh OCA], [http://pdbe.org/5hnh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hnh RCSB], [http://www.ebi.ac.uk/pdbsum/5hnh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hnh ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bpuJIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1408 ATCC 7061])</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=5hnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hnh OCA], [http://pdbe.org/5hnh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hnh RCSB], [http://www.ebi.ac.uk/pdbsum/5hnh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hnh 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 5hnh" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5hnh" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 7061]]
		+	[[Category: Large Structures]]
	[[Category: Aeschimann, W]]		[[Category: Aeschimann, W]]
	[[Category: Chau, T T.H]]		[[Category: Chau, T T.H]]

OCA at 00:02, 10 September 2016

OCA — Sat, 10 Sep 2016 00:02:40 GMT

←Older revision		Revision as of 00:02, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hnh is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain==
		+	<StructureSection load='5hnh' size='340' side='right' caption='[[5hnh]], [[Resolution\|resolution]] 1.88Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hnh]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HNH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HNH FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YPE:4-[8-(4-HYDROXYBUT-1-YN-1-YL)PYREN-1-YL]BUT-3-YN-1-YL+DIHYDROGEN+PHOSPHATE'>YPE</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=5hnh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hnh OCA], [http://pdbe.org/5hnh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hnh RCSB], [http://www.ebi.ac.uk/pdbsum/5hnh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hnh ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 A resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic pi-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.

-	~~Authors~~: ~~Probst~~, M., Aeschimann, W., Chau, T.-T.-H.~~, Langenegger, S.M~~., ~~Stocker, A., Haener, R~~.	+	Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.,Probst M, Aeschimann W, Chau TT, Langenegger SM, Stocker A, Haner R Nucleic Acids Res. 2016 Sep 6;44(15):7079-89. doi: 10.1093/nar/gkw644. Epub 2016 , Jul 15. PMID:27422870<ref>PMID:27422870</ref>

-	~~Description: Crystal structure~~ of ~~pyrene-and phenanthrene-modified DNA in complex with~~ the ~~BpuJ1 endonuclease binding domain~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Chau, T.~~-T.-~~H]]~~	+	<div class="pdbe-citations 5hnh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Aeschimann, W]]		[[Category: Aeschimann, W]]
		+	[[Category: Chau, T T.H]]
	[[Category: Haener, R]]		[[Category: Haener, R]]
-	~~[[Category: Stocker, A]]~~	+	[[Category: Langenegger, S M]]
-	[[Category: Langenegger, S.M]]	+
	[[Category: Probst, M]]		[[Category: Probst, M]]
		+	[[Category: Stocker, A]]
		+	[[Category: Dna]]
		+	[[Category: Endonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phenanthrene]]
		+	[[Category: Pyrene]]

OCA at 23:36, 3 August 2016

OCA — Wed, 03 Aug 2016 23:36:11 GMT

←Older revision		Revision as of 23:36, 3 August 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R.		Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R.

OCA at 10:03, 26 July 2016

OCA — Tue, 26 Jul 2016 10:03:21 GMT

←Older revision		Revision as of 10:03, 26 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hnh is ON HOLD ~~until Paper Publication~~	+	The entry 5hnh is ON HOLD

	Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R.		Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R.

OCA at 14:02, 3 February 2016

OCA — Wed, 03 Feb 2016 14:02:59 GMT

←Older revision		Revision as of 14:02, 3 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R.		Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R.

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

OCA — Thu, 28 Jan 2016 00:55:52 GMT

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

←Older revision

Revision as of 00:55, 28 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hnh is ON HOLD Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R. Description: Crystal structure of p...

OCA — Thu, 28 Jan 2016 00:55:51 GMT

New page: '''Unreleased structure''' The entry 5hnh is ON HOLD Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R. Description: Crystal structure of p...

New page

'''Unreleased structure'''

The entry 5hnh is ON HOLD

Authors: Probst, M., Aeschimann, W., Chau, T.-T.-H., Langenegger, S.M., Stocker, A., Haener, R.

Description: Crystal structure of pyrene-and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain
[[Category: Unreleased Structures]]
[[Category: Chau, T.-T.-H]]
[[Category: Aeschimann, W]]
[[Category: Haener, R]]
[[Category: Stocker, A]]
[[Category: Langenegger, S.M]]
[[Category: Probst, M]]