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Yorodumi- PDB-6d8f: RsAgo Ternary Complex with Guide RNA and Target DNA Containing T-... -
+Open data
-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 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Rhodobacter sphaerodes Argounaute (RsAgo) / guide RNA / target DNA / RNA-DNA heteroduplex / non-canonical base pairs and bulges | ||||||
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: 2.15 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 | 6d8f.cif.gz | 643.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d8f.ent.gz | 509.9 KB | Display | PDB format |
PDBx/mmJSON format | 6d8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/6d8f ftp://data.pdbj.org/pub/pdb/validation_reports/d8/6d8f | HTTPS FTP |
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-Related structure data
Related structure data | 6d8aC 6d8pC 6d92C 6d95C 6d9kC 6d9lC 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
-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.) 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: 5772.491 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria) #3: DNA chain | Mass: 7945.113 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria) |
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-Non-polymers , 4 types, 651 molecules
#4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-ACT / | #6: Chemical | #7: 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: 2.29 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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97921 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: 0.97921 Å / Relative weight: 1 |
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 |
-Processing
Software |
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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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