5w1z - Revision history

OCA at 14:13, 13 March 2024

OCA — Wed, 13 Mar 2024 14:13:21 GMT

←Older revision		Revision as of 14:13, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='5w1z' size='340' side='right'caption='[[5w1z]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5w1z' size='340' side='right'caption='[[5w1z]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w1z]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W1Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5W1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w1z]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W1Z FirstGlance]. <br>
-	</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=NA:SODIUM+ION'>NA</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]] 1.55Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=DI:~~2-DEOXYINOSINE-5-MONOPHOSPHATE~~'>DI</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5w20\|5w20]]~~</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=5w1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w1z OCA], [https://pdbe.org/5w1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w1z RCSB], [https://www.ebi.ac.uk/pdbsum/5w1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w1z 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=5w1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w1z OCA], [~~http~~://pdbe.org/5w1z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w1z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w1z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w1z ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Leveraging structural biology tools, we report the results of experimentsseeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from 'electrostatic' or 'base stacking' influences without considering the larger context of altered helical geometry.Circular dichroismspectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of IC pairs.X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight IC and two AT pairs)revealedan A-tract like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1'-exo (Southeastern) conformation. This contrasts with the standard B-DNA geometry with C2'-endo sugar puckers(South conformation). In contrast, the crystal structure of adecamer with only four IC pairs has a geometry similar to that of the reference duplex with eight GC and two AT pairs.The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signaturein solution and the altered mechanical properties of someinosine-containing DNAs.
-
-	Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.,Peters JP, Kowal EA, Pallan PS, Egli M, Maher LJ 3rd J Biomol Struct Dyn. 2017 Aug 18:1-60. doi: 10.1080/07391102.2017.1369164. PMID:28818035<ref>PMID:28818035</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5w1z" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Egli, M~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Pallan, P S~~]]	+	[[Category: Egli M]]
-	[[Category: ~~Circular dichroism of modified dna]]~~	+	[[Category: Pallan PS]]
-	~~[[Category: Deoxyinonsine]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna crystal structure]]~~	+
-	~~[[Category: Inosine~~]]	+

OCA at 08:47, 30 September 2020

OCA — Wed, 30 Sep 2020 08:47:22 GMT

←Older revision		Revision as of 08:47, 30 September 2020
Line 1:		Line 1:

	==Crystal Structure of inosine-substituted decamer duplex DNA (I4)==		==Crystal Structure of inosine-substituted decamer duplex DNA (I4)==
-	<StructureSection load='5w1z' size='340' side='right' caption='[[5w1z]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5w1z' size='340' side='right'caption='[[5w1z]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w1z]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W1Z OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w1z]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W1Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5W1Z 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=NA:SODIUM+ION'>NA</scene></td></tr>	+	</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=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w20\|5w20]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5w20\|5w20]]</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=5w1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w1z OCA], [http://pdbe.org/5w1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w1z RCSB], [http://www.ebi.ac.uk/pdbsum/5w1z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w1z 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=5w1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w1z OCA], [http://pdbe.org/5w1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w1z RCSB], [http://www.ebi.ac.uk/pdbsum/5w1z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w1z ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Pallan, P S]]		[[Category: Pallan, P S]]

OCA: Protected "5w1z" [edit=sysop:move=sysop]

OCA — Wed, 30 Aug 2017 04:19:20 GMT

Protected "5w1z" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:19, 30 August 2017

OCA: New page: ==Crystal Structure of inosine-substituted decamer duplex DNA (I4)==
OCA — Wed, 30 Aug 2017 04:19:18 GMT

New page: ==Crystal Structure of inosine-substituted decamer duplex DNA (I4)== <StructureSection load='5w1z' size='340' side='right' caption='5w1z, resolution 1.55Å' scene=...

New page

==Crystal Structure of inosine-substituted decamer duplex DNA (I4)==
<StructureSection load='5w1z' size='340' side='right' caption='[[5w1z]], [[Resolution|resolution]] 1.55Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5w1z]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W1Z 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=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5w20|5w20]]</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=5w1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w1z OCA], [http://pdbe.org/5w1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w1z RCSB], [http://www.ebi.ac.uk/pdbsum/5w1z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w1z ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Leveraging structural biology tools, we report the results of experimentsseeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from 'electrostatic' or 'base stacking' influences without considering the larger context of altered helical geometry.Circular dichroismspectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of IC pairs.X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight IC and two AT pairs)revealedan A-tract like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1'-exo (Southeastern) conformation. This contrasts with the standard B-DNA geometry with C2'-endo sugar puckers(South conformation). In contrast, the crystal structure of adecamer with only four IC pairs has a geometry similar to that of the reference duplex with eight GC and two AT pairs.The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signaturein solution and the altered mechanical properties of someinosine-containing DNAs.

Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.,Peters JP, Kowal EA, Pallan PS, Egli M, Maher LJ 3rd J Biomol Struct Dyn. 2017 Aug 18:1-60. doi: 10.1080/07391102.2017.1369164. PMID:28818035<ref>PMID:28818035</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5w1z" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Egli, M]]
[[Category: Pallan, P S]]
[[Category: Circular dichroism of modified dna]]
[[Category: Deoxyinonsine]]
[[Category: Dna]]
[[Category: Dna crystal structure]]
[[Category: Inosine]]