This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


192d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:26, 7 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
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==
+
-
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''
+

Current revision

RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)

PDB ID 192d

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/192d"
Personal tools