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Yorodumi- PDB-4q2d: Crystal Structure of CRISPR-Associated protein in complex with 2'... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q2d | ||||||
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Title | Crystal Structure of CRISPR-Associated protein in complex with 2'-Deoxyadenosine 5'-Triphosphate | ||||||
Components | CRISPR-associated helicase Cas3 | ||||||
Keywords | HYDROLASE / RecA / HD nuclease | ||||||
Function / homology | Function and homology information helicase activity / defense response to virus / hydrolase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermobaculum terrenum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.771 Å | ||||||
Authors | Gong, B. / Shin, M. / Sun, J. / van der Oost, J. / Kim, J.-S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3. Authors: Gong, B. / Shin, M. / Sun, J. / Jung, C.H. / Bolt, E.L. / van der Oost, J. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q2d.cif.gz | 379.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q2d.ent.gz | 306.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q2d ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q2d | HTTPS FTP |
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-Related structure data
Related structure data | 4q2cSC 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
#1: Protein | Mass: 105150.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobaculum terrenum (bacteria) / Strain: ATCC BAA-798 / Gene: Tter_1895 / Production host: Escherichia coli (E. coli) / References: UniProt: D1CGD0 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-DTP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.2M Sodium Chloride, 0.1M Sodium phosphate monobasic monohydrate, 0.1M Potassium phosphate monobasic, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.771→100 Å / Num. all: 29838 / Num. obs: 28764 / % possible obs: 96.4 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Biso Wilson estimate: 39.24 Å2 |
Reflection shell | Resolution: 2.8→2.85 Å / % possible all: 83.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4q2c Resolution: 2.771→45.655 Å / FOM work R set: 0.8402 / SU ML: 0.4 / σ(F): 1.46 / Phase error: 23.27 / Stereochemistry target values: ML
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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 max: 267.25 Å2 / Biso mean: 47.44 Å2 / Biso min: 19.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.771→45.655 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -28.7902 Å / Origin y: 28.5366 Å / Origin z: -3.7592 Å
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Refinement TLS group | Selection details: ALL |