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- PDB-8kak: Crystal structure of SpyCas9 in complex with sgRNA and 18nt target DNA -
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Open data
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Basic information
Entry | Database: PDB / ID: 8kak | ||||||
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Title | Crystal structure of SpyCas9 in complex with sgRNA and 18nt target DNA | ||||||
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![]() | RNA BINDING PROTEIN/RNA/DNA / Nuclease / RNA BINDING PROTEIN-RNA-DNA 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, Y. / Chen, J. / Liu, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Trans-nuclease activity of Cas9 activated by DNA or RNA target binding. Authors: Chen, J. / Chen, Y. / Huang, L. / Lin, X. / Chen, H. / Xiang, W. / Liu, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 690.1 KB | Display | ![]() |
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PDB format | ![]() | 544.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 552.1 KB | Display | ![]() |
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Full document | ![]() | 856 KB | Display | |
Data in XML | ![]() | 139.8 KB | Display | |
Data in CIF | ![]() | 187.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kagC ![]() 8kahC ![]() 8kaiC ![]() 8kajC ![]() 8kalC ![]() 8kamC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-DNA chain , 2 types, 4 molecules CGDH
#3: DNA chain | Mass: 7924.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TS Source: (synth.) ![]() #4: DNA chain | Mass: 3394.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: NTS Source: (synth.) ![]() |
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-RNA chain / Protein , 2 types, 4 molecules AEBF
#1: RNA chain | Mass: 31610.740 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Protein | Mass: 158588.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cas9, csn1, SPy_1046 / Production host: ![]() ![]() References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
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-Non-polymers , 2 types, 8 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.15 M Ammonium sulfate, 0.1 M MES pH 6.0, 14.75% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 52766 / % possible obs: 94.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 30.01 Å2 / Rpim(I) all: 0.176 / Net I/σ(I): 4.11 |
Reflection shell | Resolution: 3.6→3.72 Å / Redundancy: 2.6 % / Num. unique obs: 2595 / Rpim(I) all: 0.708 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→24.97 Å
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Refine LS restraints |
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LS refinement shell |
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