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.


369d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:26, 21 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:369d.gif|left|200px]]<br /><applet load="369d" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="369d, resolution 1.900&Aring;" />
 
-
'''STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPCPCPGPCPGPGPG)'''<br />
 
-
==Overview==
+
==STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPCPCPGPCPGPGPG)==
-
We have determined the structure of the synthetic DNA octamer d(pCpCpCpGpCpGpGpG) in five different crystal forms by single crystal X-ray diffraction. One crystal belongs to the space group P4(3)2(1)2 with a = b = 41.77, c = 25.15 A, whereas all others have the space group P2(1)2(1)2(1) with progressively decreasing unit cell volumes. In all crystals the octamer forms duplexes of A-DNA and all crystals display a similar packing mode, typical for A-DNA. The structure of the duplex varies from loose to very compact when going from one crystal form to another. The most compact form exhibits a volume of 995 A3 per base pair. Such a high density has never been found in A-DNA, being more characteristic of Z-DNA crystals. A comparison of the most with the least compact forms gives a RMS value of 1.7 A, with the distance between the phosphate centers through the major groove being almost twice shorter in the compact form. The phosphate-phosphate separation across the major groove in the compact form is extremely small, 0.7 A. The helical parameters also vary significantly in the various crystal forms. Differences in the helical twist can reach 13 degrees in the same step of the octamer in different crystal forms. The results prove that A-DNA is structurally very variable and demonstrate that the local structure of the same DNA fragment can strongly depend on the crystal environment.
+
<StructureSection load='369d' size='340' side='right'caption='[[369d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[369d]] is a 2 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=369D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=369D FirstGlance]. <br>
-
369D is a [http://en.wikipedia.org/wiki/Protein_complex 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=369D OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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=369d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=369d OCA], [https://pdbe.org/369d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=369d RCSB], [https://www.ebi.ac.uk/pdbsum/369d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=369d ProSAT]</span></td></tr>
-
==Reference==
+
</table>
-
Structural variability of A-DNA in crystals of the octamer d(pCpCpCpGpCpGpGpG), Fernandez LG, Subirana JA, Verdaguer N, Pyshnyi D, Campos L, Malinina L, J Biomol Struct Dyn. 1997 Aug;15(1):151-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9283988 9283988]
+
__TOC__
-
[[Category: Protein complex]]
+
</StructureSection>
-
[[Category: Campos, L.]]
+
[[Category: Large Structures]]
-
[[Category: Fernandez, L Campos L G.]]
+
[[Category: Synthetic construct]]
-
[[Category: Pyshnyi, D.]]
+
[[Category: Campos L]]
-
[[Category: Subirana, J A.]]
+
[[Category: Fernandez LG]]
-
[[Category: Verdaguer, N.]]
+
[[Category: Pyshnyi D]]
-
[[Category: a-dna]]
+
[[Category: Subirana JA]]
-
[[Category: double helix]]
+
[[Category: Verdaguer N]]
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:02:23 2008''
+

Current revision

STRUCTURAL VARIABILITY OF A-DNA IN CRYSTALS OF THE OCTAMER D(PCPCPCPGPCPGPGPG)

PDB ID 369d

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/369d"
Personal tools