+Open data
-Basic information
Entry | Database: PDB / ID: 7ei1 | ||||||
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Title | Structure of Pyrococcus furiosus Cas1Cas2 complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CRISPR / adaptation | ||||||
Function / homology | Function and homology information maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus COM1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | ||||||
Authors | Yu, Y. / Chen, Q. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2021 Title: A distinct structure of Cas1-Cas2 complex provides insights into the mechanism for the longer spacer acquisition in Pyrococcus furiosus. Authors: Tang, D. / Li, H. / Wu, C. / Jia, T. / He, H. / Yao, S. / Yu, Y. / Chen, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ei1.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ei1.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 7ei1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/7ei1 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7ei1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 37539.426 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: cas1, PFC_04810 / Production host: Escherichia coli (E. coli) References: UniProt: I6TWX9, Hydrolases; Acting on ester bonds #2: Protein | Mass: 9992.677 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: cas2, PFC_04805 / Production host: Escherichia coli (E. coli) References: UniProt: I6V1H0, Hydrolases; Acting on ester bonds |
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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: 4.42 Å3/Da / Density % sol: 72.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% w/v polyethylene glycol 6000, 6% v/v ethylene glycol, 0.1M citric acid pH 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→50 Å / Num. obs: 107906 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 42.49 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.063 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.9→3.97 Å / Num. unique obs: 5377 / CC1/2: 0.957 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WJ0,4TN0 Resolution: 3.9→36.53 Å / SU ML: 0.6278 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.4845 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: 52.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→36.53 Å
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Refine LS restraints |
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LS refinement shell |
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