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- PDB-6k4s: Crystal structure of xCas9 in complex with sgRNA and DNA (TGC PAM) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k4s | ||||||
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Title | Crystal structure of xCas9 in complex with sgRNA and DNA (TGC PAM) | ||||||
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![]() | HYDROLASE/DNA/RNA / endonuclease / HYDROLASE-DNA-RNA complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, W. / Zhang, H. / Zhang, Y. / Wang, Y. / Gan, J. / Ji, Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease. Authors: Chen, W. / Zhang, H. / Zhang, Y. / Wang, Y. / Gan, J. / Ji, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 646.2 KB | Display | ![]() |
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PDB format | ![]() | 526.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.7 KB | Display | ![]() |
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Full document | ![]() | 511.4 KB | Display | |
Data in XML | ![]() | 49.9 KB | Display | |
Data in CIF | ![]() | 69.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k3zC ![]() 6k4pC ![]() 6k4qC ![]() 6k4uC ![]() 6k57C ![]() 4un3S S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 158574.844 Da / Num. of mol.: 1 Mutation: D10A, C80L, A262T, R324L, S409T, E480K, E543D, C574E, M694I, H840A, E1219V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cas9 / Production host: ![]() ![]() References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 26788.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: DNA chain | Mass: 8592.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: DNA chain | Mass: 3685.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 85 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: AGILENT EOS CCD / Detector: CCD / Date: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 43368 / % possible obs: 98.8 % / Redundancy: 6.5 % / CC1/2: 1 / Rpim(I) all: 0.071 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5.5 % / Num. unique obs: 4176 / CC1/2: 0.543 / Rpim(I) all: 0.578 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UN3 Resolution: 3.01→49.25 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.823 / SU B: 54.535 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.534 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 70.805 Å2
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Refinement step | Cycle: 1 / Resolution: 3.01→49.25 Å
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Refine LS restraints |
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