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Yorodumi- PDB-5xvp: E. fae Cas1-Cas2/prespacer/target ternary complex revealing the f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xvp | |||||||||||||||
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Title | E. fae Cas1-Cas2/prespacer/target ternary complex revealing the fully integrated states | |||||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / CRISPR / Cas | |||||||||||||||
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 | Enterococcus faecalis TX0027 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | |||||||||||||||
Authors | Xiao, Y. / Ng, S. / Nam, K.H. / Ke, A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nature / Year: 2017 Title: How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration. Authors: Xiao, Y. / Ng, S. / Hyun Nam, K. / Ke, A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xvp.cif.gz | 748.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xvp.ent.gz | 612.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/5xvp ftp://data.pdbj.org/pub/pdb/validation_reports/xv/5xvp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-CRISPR-associated ... , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 33492.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis TX0027 (bacteria) Gene: cas1, HMPREF9501_02814 / Production host: Escherichia coli (E. coli) References: UniProt: E6GPD7, Hydrolases; Acting on ester bonds #2: Protein | Mass: 12977.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis TX0027 (bacteria) Gene: cas2, HMPREF9501_02813 / Production host: Escherichia coli (E. coli) References: UniProt: E6GPD6, Hydrolases; Acting on ester bonds |
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-DNA chain , 3 types, 4 molecules GHIJ
#3: DNA chain | Mass: 22406.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria) |
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#4: DNA chain | Mass: 22548.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria) |
#5: DNA chain | Mass: 2706.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Enterococcus faecalis TX0027 (bacteria) |
-Non-polymers , 2 types, 4 molecules
#6: Chemical | #7: 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: 4.24 Å3/Da / Density % sol: 71 % |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium acetate, 100 mM sodium citrate, pH 4.8, and 4-7% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 68246 / % possible obs: 99.1 % / Redundancy: 5.1 % / Net I/σ(I): 8.6 |
-Processing
Software |
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Refinement | Resolution: 3→49.03 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 41.415 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.857 Å2
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Refinement step | Cycle: 1 / Resolution: 3→49.03 Å
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Refine LS restraints |
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