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- PDB-6d8f: RsAgo Ternary Complex with Guide RNA and Target DNA Containing T-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d8f | ||||||
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Title | RsAgo Ternary Complex with Guide RNA and Target DNA Containing T-T Bulge Within the Seed Segment | ||||||
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Function / homology | ![]() clearance of foreign intracellular DNA / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, Y. / Esyunina, D. / Olovnikov, I. / Teplova, M. / Patel, D.J. | ||||||
![]() | ![]() Title: Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. Authors: Liu, Y. / Esyunina, D. / Olovnikov, I. / Teplova, M. / Kulbachinskiy, A. / Aravin, A.A. / Patel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 643.7 KB | Display | ![]() |
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PDB format | ![]() | 509.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6d8aC ![]() 6d8pC ![]() 6d92C ![]() 6d95C ![]() 6d9kC ![]() 6d9lC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / RNA chain / DNA chain , 3 types, 6 molecules AFCHGJ
#1: Protein | Mass: 89038.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 17025 / ATH 2.4.3 / Gene: Rsph17025_3694 / Production host: ![]() ![]() ![]() #2: RNA chain | Mass: 5772.491 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() #3: DNA chain | Mass: 7945.113 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() |
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-Non-polymers , 4 types, 651 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MPD / ( ![]() #5: Chemical | ChemComp-ACT / | ![]() #6: Chemical | #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion Details: 40% MPD, 30 mM magnesium acetate, 50 mM sodium cacodylate pH 5.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→50 Å / Num. obs: 100379 / % possible obs: 99.9 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.732 / % possible all: 100 |
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Processing
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Refinement | Resolution: 2.15→42.3 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.15→42.3 Å
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