1g4q
From Proteopedia
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|PDB= 1g4q |SIZE=350|CAPTION= <scene name='initialview01'>1g4q</scene>, resolution 1.15Å | |PDB= 1g4q |SIZE=350|CAPTION= <scene name='initialview01'>1g4q</scene>, resolution 1.15Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |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> | ||
}} | }} | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Han, G W.]] | [[Category: Han, G W.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: MPD]] | ||
[[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 | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:36:33 2008'' |
Revision as of 17:36, 30 March 2008
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| , resolution 1.15Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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
1G4Q is a Protein complex structure of sequences from [1]. 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
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