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- PDB-6d92: Ternary RsAgo 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: 6d92 | ||||||
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Title | Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-A non-canonical pair at position 3 | ||||||
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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 | ![]() | 371.2 KB | Display | ![]() |
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PDB format | ![]() | 288 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.8 KB | Display | ![]() |
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Full document | ![]() | 542.5 KB | Display | |
Data in XML | ![]() | 64.1 KB | Display | |
Data in CIF | ![]() | 95.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d8aC ![]() 6d8fC ![]() 6d8pC ![]() 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
-DNA chain , 2 types, 2 molecules GJ
#3: DNA chain | Mass: 5789.762 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
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#4: DNA chain | Mass: 6423.161 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
-Protein / RNA chain , 2 types, 4 molecules AFCH
#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.) ![]() |
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-Non-polymers , 4 types, 855 molecules ![](data/chem/img/ACT.gif)
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![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ACT / #6: Chemical | #7: Chemical | ChemComp-MPD / ( | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
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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: 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: 1.81→70 Å / Num. obs: 160184 / % possible obs: 93.8 % / Redundancy: 4.3 % / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.81→1.87 Å |
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Processing
Software |
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Refinement | Resolution: 1.81→42.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.377 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.138 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: 133.36 Å2 / Biso mean: 40.667 Å2 / Biso min: 19.24 Å2
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Refinement step | Cycle: final / Resolution: 1.81→42.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.809→1.855 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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