1g4q

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
[[Image:1g4q.gif|left|200px]]
[[Image:1g4q.gif|left|200px]]
-
{{Structure
+
<!--
-
|PDB= 1g4q |SIZE=350|CAPTION= <scene name='initialview01'>1g4q</scene>, resolution 1.15&Aring;
+
The line below this paragraph, containing "STRUCTURE_1g4q", creates the "Structure Box" on the page.
-
|SITE=
+
You may change the PDB parameter (which sets the PDB file loaded into the applet)
-
|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
+
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-
|ACTIVITY=
+
or leave the SCENE parameter empty for the default display.
-
|GENE=
+
-->
-
|DOMAIN=
+
{{STRUCTURE_1g4q| PDB=1g4q | SCENE= }}
-
|RELATEDENTRY=
+
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1g4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g4q OCA], [http://www.ebi.ac.uk/pdbsum/1g4q PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1g4q RCSB]</span>
+
-
}}
+
'''RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG'''
'''RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG'''
Line 19: Line 16:
==About this Structure==
==About this Structure==
-
1G4Q 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=1G4Q OCA].
+
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G4Q OCA].
==Reference==
==Reference==
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11173466 11173466]
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11173466 11173466]
-
[[Category: Protein complex]]
 
[[Category: Han, G W.]]
[[Category: Han, G W.]]
-
[[Category: direct method]]
+
[[Category: Direct method]]
-
[[Category: polypurine tract of hiv-1]]
+
[[Category: Polypurine tract of hiv-1]]
-
[[Category: rna/dna hybrid]]
+
[[Category: Rna/dna hybrid]]
-
 
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 17:08:14 2008''
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:36:33 2008''
+

Revision as of 14:08, 2 May 2008

Image:1g4q.gif

Template:STRUCTURE 1g4q

RNA/DNA HYBRID DECAMER OF CAAAGAAAAG/CTTTTCTTTG


Overview

For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the RNA/DNA decamer molecule using 1.15 A data, which is just on the resolution edge of what might work with direct methods. Atomic positions for 96% of the entire molecule, containing 514 non-H atoms including three Ca(2+) ions, were easily interpreted from a Fourier map based on the 'Shake-and-Bake' minimal function and CROQUE phase-refinement program. Only six atoms, primarily in the sugar linkage, were missing in this Fourier map. At present, the R factor of the model is 0.143 (R(free) = 0.186) for the 562 non-H atom sites located. The conformation of the RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This paper presents the methodology used in solving this structure.

About this Structure

Full crystallographic information is available from OCA.

Reference

Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:11173466 Page seeded by OCA on Fri May 2 17:08:14 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1g4q"
Personal tools