+Open data
-Basic information
Entry | Database: PDB / ID: 6o6s | ||||||
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Title | Crystal structure of Apo Csm6 | ||||||
Components | Csm6 | ||||||
Keywords | IMMUNE SYSTEM / Type III-A CRISPR-Cas system / Csm6 | ||||||
Function / homology | CRISPR system endoribonuclease Csx1 / CRISPR-associated protein DxTHG, conserved site / CRISPR system endoribonuclease Csx1-like / CRISPR system endoribonuclease Csx1, HEPN domain / : / CRISPR system endoribonuclease Csx1-like domain-containing protein Function and homology information | ||||||
Biological species | Thermococcus onnurineus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å | ||||||
Authors | Jia, N. / Patel, D.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2019 Title: CRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA4Cleavage with ApA>p Formation Terminating RNase Activity. Authors: Jia, N. / Jones, R. / Yang, G. / Ouerfelli, O. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o6s.cif.gz | 178.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o6s.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 6o6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o6s_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 6o6s_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 6o6s_validation.xml.gz | 29 KB | Display | |
Data in CIF | 6o6s_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/6o6s ftp://data.pdbj.org/pub/pdb/validation_reports/o6/6o6s | HTTPS FTP |
-Related structure data
Related structure data | 6o6tC 6o6vC 6o6xC 6o6yC 6o6zC 6o70C 6o71C 6ov0C 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: Protein | Mass: 49795.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: TON_0898 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC3 |
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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: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% PEG 8K, 0.2 M NaCl, 0.1 M Na/K phosphate pH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→48.53 Å / Num. obs: 25271 / Rpim(I) all: 0.068 |
Reflection shell | Resolution: 2.65→2.74 Å / Num. unique obs: 2748 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.65→48.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 16.771 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / 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: 71.028 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→48.53 Å
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Refine LS restraints |
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