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Yorodumi- PDB-6k4q: Crystal structure of xCas9 in complex with sgRNA and DNA (CGG PAM) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k4q | ||||||
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Title | Crystal structure of xCas9 in complex with sgRNA and DNA (CGG PAM) | ||||||
Components |
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Keywords | HYDROLASE/DNA/RNA / endonuclease / HYDROLASE-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 serotype M1 (bacteria) Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Chen, W. / Zhang, H. / Zhang, Y. / Wang, Y. / Gan, J. / Ji, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Plos Biol. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k4q.cif.gz | 668.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k4q.ent.gz | 540.5 KB | Display | PDB format |
PDBx/mmJSON format | 6k4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/6k4q ftp://data.pdbj.org/pub/pdb/validation_reports/k4/6k4q | HTTPS FTP |
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-Related structure data
Related structure data | 6k3zC 6k4pC 6k4sC 6k4uC 6k57C 4un3S 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
-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 8568.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
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#3: DNA chain | Mass: 3710.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
-RNA chain / Protein , 2 types, 2 molecules AB
#1: RNA chain | Mass: 26788.984 Da / Num. of mol.: 1 Mutation: D10A, C80L, A262T, R324L, S409T, E480K, E543D, C574E, M694I, H840A, E1219V Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria) |
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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.) Streptococcus pyogenes serotype M1 (bacteria) Gene: Cas9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds |
-Non-polymers , 2 types, 108 molecules
#5: Chemical | ChemComp-PO4 / #6: 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: 2.89 Å3/Da / Density % sol: 57.45 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
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: 2.7→50 Å / Num. obs: 60255 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rpim(I) all: 0.063 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.7 % / Num. unique obs: 5992 / CC1/2: 0.578 / Rpim(I) all: 0.506 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UN3 Resolution: 2.7→49.38 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.869 / SU B: 34.022 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 1.752 / ESU R Free: 0.381 / 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: 47.669 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→49.38 Å
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Refine LS restraints |
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