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- PDB-6d8a: RsAgo Ternary Complex with guide RNA and Target DNA Containing A-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d8a | ||||||
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Title | RsAgo Ternary Complex with guide RNA and Target DNA Containing A-A Bulge Within the Seed Segment of the Target Strand | ||||||
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![]() | RNA BINDING PROTEIN / Rhodobacter sphaerodes Argounaute (RsAgo) / guide RNA / target DNA / RNA-DNA heteroduplex / non-canonical base pairs and bulges | ||||||
Function / homology | ![]() clearance of foreign intracellular DNA / DNA binding / RNA binding / metal ion binding 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 | ![]() | 636.2 KB | Display | ![]() |
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PDB format | ![]() | 504.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 520.2 KB | Display | ![]() |
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Full document | ![]() | 549.1 KB | Display | |
Data in XML | ![]() | 61.7 KB | Display | |
Data in CIF | ![]() | 86.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d8fC ![]() 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: 7963.142 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() |
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-Non-polymers , 4 types, 429 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MPD / ( #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.19 % |
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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: Apr 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 88612 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.754 / % possible all: 100 |
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Processing
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Refinement | Resolution: 2.251→42.665 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.251→42.665 Å
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