+Open data
-Basic information
Entry | Database: PDB / ID: 6k2e | ||||||
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Title | Crystal structure of cas2 | ||||||
Components | CRISPR/cas2 protein | ||||||
Keywords | RNA BINDING PROTEIN / crispr / cas2 | ||||||
Function / homology | Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | Pyrococcus horikoshii OT3 (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Mo, X. / Bi, M. / Yuan, A.Y. | ||||||
Citation | Journal: To be published Title: Structural insight into endonuclease CRISPR-associated Cas2 protein Authors: Mo, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k2e.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k2e.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/6k2e ftp://data.pdbj.org/pub/pdb/validation_reports/k2/6k2e | HTTPS FTP |
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-Related structure data
Related structure data | 6jhzC 5g4dS C: citing same article (ref.) S: Starting model for refinement |
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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: 10472.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Production host: Escherichia coli (E. coli) #2: 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: 2.8 Å3/Da / Density % sol: 56.07 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop Details: 0.02M Magnesium, 16.5% v/v 2-propanol, 0.1M Sodium Cacodylate pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25.42 Å / Num. obs: 5885 / % possible obs: 99.73 % / Redundancy: 8 % / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 587 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G4D Resolution: 2.8→25.42 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→25.42 Å
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Refine LS restraints |
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LS refinement shell |
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