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Yorodumi- PDB-6aeg: Crystal structure of xCas9 in complex with sgRNA and target DNA (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aeg | ||||||
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Title | Crystal structure of xCas9 in complex with sgRNA and target DNA (GAT PAM) | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA/RNA / enzyme / DNA / nuclease / DNA BINDING PROTEIN-DNA-RNA complex | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å | ||||||
Authors | Guo, M. / Ren, K. / Zhu, Y. / Huang, Z. | ||||||
Citation | Journal: Cell Res. / Year: 2019 Title: Structural insights into a high fidelity variant of SpCas9. Authors: Guo, M. / Ren, K. / Zhu, Y. / Tang, Z. / Wang, Y. / Zhang, B. / Huang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aeg.cif.gz | 354.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aeg.ent.gz | 273.3 KB | Display | PDB format |
PDBx/mmJSON format | 6aeg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/6aeg ftp://data.pdbj.org/pub/pdb/validation_reports/ae/6aeg | HTTPS FTP |
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-Related structure data
Related structure data | 6aebSC S: Starting model for refinement 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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Unit cell |
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-Components
#1: RNA chain | Mass: 32269.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
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#2: DNA chain | Mass: 8567.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
#3: DNA chain | Mass: 3396.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
#4: Protein | Mass: 158538.844 Da / Num. of mol.: 1 Mutation: D10A, A263T, R324L, S409I, E480K, E543D, M694I, H840A, E1219V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Hepes, pH 7.5, 0.2M Ammonium sulfate, 10% ispropanol, 16% (w/v) PEG4000, 30%(v/v) (+/-)-2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 60687 / % possible obs: 94.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.7→2.75 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AEB Resolution: 2.701→44.972 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.73 Details: The data completeness is 94.1%, calculated by software HKL2000.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.701→44.972 Å
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Refine LS restraints |
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LS refinement shell |
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