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Yorodumi- PDB-6d9l: Ternary RsAgo Complex with Guide RNA and Target DNA Containing G-... -
+Open data
-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 | ||||||
Components |
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Keywords | 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 | Function and homology information clearance of foreign intracellular DNA / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) Rhodobacter sphaeroides ATCC 17025 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Liu, Y. / Esyunina, D. / Olovnikov, I. / Teplova, M. / Patel, D.J. | ||||||
Citation | Journal: Cell Rep / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d9l.cif.gz | 348.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d9l.ent.gz | 270.4 KB | Display | PDB format |
PDBx/mmJSON format | 6d9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9l ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9l | HTTPS FTP |
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-Related structure data
Related structure data | 6d8aC 6d8fC 6d8pC 6d92C 6d95C 6d9kC C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) (bacteria) Strain: ATCC 17025 / ATH 2.4.3 / Gene: Rsph17025_3694 / Production host: Escherichia coli (E. coli) / References: UniProt: A4WYU7 #2: RNA chain | Mass: 5788.491 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria) #3: DNA chain | Mass: 7345.742 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria) #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
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 |
-Processing
Software |
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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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