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- PDB-6d9l: Ternary RsAgo Complex with Guide RNA and Target DNA Containing G-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d9l | ||||||
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Title | Ternary RsAgo Complex with Guide RNA and Target DNA Containing G-A Non-canonical Pair | ||||||
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![]() | RNA BINDING PROTEIN/RNA/DNA / guide RNA. target DNA. RNA-DNA heteroduplex. non-canonical base pairs and bulges / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex | ||||||
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 | ![]() | 348.4 KB | Display | ![]() |
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PDB format | ![]() | 270.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.4 KB | Display | ![]() |
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Full document | ![]() | 495.5 KB | Display | |
Data in XML | ![]() | 53.8 KB | Display | |
Data in CIF | ![]() | 74.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d8aC ![]() 6d8fC ![]() 6d8pC ![]() 6d92C ![]() 6d95C ![]() 6d9kC 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
#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: 5788.491 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() #3: DNA chain | Mass: 7345.742 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % |
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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: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 55738 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.722 / % possible all: 97.8 |
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Processing
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Refinement | Resolution: 2.6→41.67 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.342 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.22 Å2 / Biso mean: 51.726 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 2.6→41.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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