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- PDB-6k4p: Crystal structure of xCas9 in complex with sgRNA and DNA (TGG PAM) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k4p | ||||||
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Title | Crystal structure of xCas9 in complex with sgRNA and DNA (TGG 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 | ![]() | 667.1 KB | Display | ![]() |
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PDB format | ![]() | 540 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6k3zC ![]() 6k4qC ![]() 6k4sC ![]() 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
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 8552.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 3725.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-RNA chain / Protein , 2 types, 2 molecules AB
#1: RNA chain | Mass: 27094.166 Da / Num. of mol.: 1 Mutation: D10A, C80L, A262T, R324L, S409T, E480K, E543D, C574E, M694I, H840A, E1219V Source method: obtained synthetically / Source: (synth.) ![]() |
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#4: Protein | Mass: 158574.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Cas9 / Production host: ![]() ![]() References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
-Non-polymers , 2 types, 27 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.23 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M 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: 2.9→50 Å / Num. obs: 48459 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.961 / Rpim(I) all: 0.116 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.9 % / Num. unique obs: 4780 / CC1/2: 0.376 / Rpim(I) all: 0.7 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UN3 Resolution: 2.9→46.77 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.871 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→46.77 Å
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Refine LS restraints |
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