192d: Difference between revisions

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~~[[Image:192d.gif|left|200px]]~~

~~{{Structure~~

==RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)==

~~|PDB~~= 192d ~~|SIZE~~=~~350|CAPTION~~= ~~<scene name~~='~~initialview01'>~~192d~~</scene>~~, resolution 1.~~920~~Å

~~|SITE~~=

== Structural highlights ==

~~|LIGAND~~= <~~scene name~~='~~pdbligand~~=DC:~~2'~~-~~DEOXYCYTIDINE-5~~'~~-MONOPHOSPHATE'~~>DC</~~scene~~>, <~~scene name~~='~~pdbligand~~=DG:~~2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'~~>DG</~~scene~~>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>

<table><tr><td colspan='2'>[[192d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=192D OCA]. For a guided tour on the structure components use [https://proteopedia.org/fgij/fg.htm?mol=192D FirstGlance].

~~|ACTIVITY~~=

</td></tr><tr id='method'><td class="sblockLbl">[[Empirical_models|Method:]]</td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.92Å</td></tr>

~~|GENE~~=

<tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>

~~|DOMAIN=~~

<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[https://proteopedia.org/fgij/fg.htm?mol=192d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=192d OCA], [https://pdbe.org/192d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=192d RCSB], [https://www.ebi.ac.uk/pdbsum/192d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=192d ProSAT]</td></tr>

~~|RELATEDENTRY=~~

</table>

~~|RESOURCES~~=[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=192d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=192d OCA], [~~http~~://~~www~~.~~ebi.ac.uk/pdbsum~~/192d ~~PDBsum~~], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=192d RCSB]~~~~

__TOC__

}}

</StructureSection>

[[Category: Large Structures]]

~~'''RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)'''~~

[[Category: Huynh-Dinh T]]

[[Category: Malinina L]]

[[Category: Salas X]]

~~==Overview==~~

[[Category: Subirana JA]]

We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.

[[Category: Urpi L]]

~~==About this Structure==~~

~~192D is a~~ [~~[Protein complex]] structure of sequences from [http~~://en.~~wikipedia~~.~~org~~/~~wiki~~/ ]~~. Full crystallographic information is available from~~ [~~http~~://~~oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin~~/~~ocashort~~?id=~~192D OCA~~].

~~==Reference==~~

~~Recombination-like structure of d(CCGCGG)., Malinina L, Urpi L, Salas X, Huynh-Dinh T, Subirana JA, J Mol Biol. 1994 Oct 28;243(3):484-93. PMID:[http:~~/~~/www.ncbi.nlm.nih.gov/pubmed/7966274 7966274]~~

[[Category: ~~Protein complex~~]]

[[Category: Huynh-Dinh, T.]]

[[Category: Malinina, L.]]

[[Category: Salas, X.]]

[[Category: Subirana~~, J A.~~]]

[[Category: Urpi, L~~.]]~~

~~[[Category: double helix~~]]

~~[[Category: flipped-out base]]~~

~~[[Category: z-dna]]~~

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:29:51 2008''~~

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@@ Line 1: / Line 1: @@
-[[Image:192d.gif|left|200px]]
- {{Structure
+==RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)==
-|PDB= 192d |SIZE=350|CAPTION= <scene name='initialview01'>192d</scene>, resolution 1.920&Aring;
+<StructureSection load='192d' size='340' side='right'caption='[[192d]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
+<table><tr><td colspan='2'>[[192d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=192D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=192D FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.92&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=192d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=192d OCA], [https://pdbe.org/192d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=192d RCSB], [https://www.ebi.ac.uk/pdbsum/192d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=192d ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=192d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=192d OCA], [http://www.ebi.ac.uk/pdbsum/192d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=192d RCSB]</span>
+__TOC__
-}}
+</StructureSection>
+[[Category: Large Structures]]
-'''RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)'''
+[[Category: Huynh-Dinh T]]
+[[Category: Malinina L]]
+[[Category: Salas X]]
-==Overview==
+[[Category: Subirana JA]]
-We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F &gt; or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.
+[[Category: Urpi L]]
-==About this Structure==
-D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=192D OCA].
-==Reference==
-Recombination-like structure of d(CCGCGG)., Malinina L, Urpi L, Salas X, Huynh-Dinh T, Subirana JA, J Mol Biol. 1994 Oct 28;243(3):484-93. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7966274 7966274]
-[[Category: Protein complex]]
-[[Category: Huynh-Dinh, T.]]
-[[Category: Malinina, L.]]
-[[Category: Salas, X.]]
-[[Category: Subirana, J A.]]
-[[Category: Urpi, L.]]
-[[Category: double helix]]
-[[Category: flipped-out base]]
-[[Category: z-dna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:29:51 2008''