+Open data
-Basic information
Entry | Database: PDB / ID: 5id6 | ||||||
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Title | Structure of Cpf1/RNA Complex | ||||||
Components |
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Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain Similarity search - Domain/homology | ||||||
Biological species | Lachnospiraceae bacterium ND2006 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.382 Å | ||||||
Authors | Dong, D. / Ren, K. / Qiu, X. / Wang, J. / Huang, Z. | ||||||
Citation | Journal: Nature / Year: 2016 Title: The crystal structure of Cpf1 in complex with CRISPR RNA Authors: Dong, D. / Ren, K. / Qiu, X. / Zheng, J. / Guo, M. / Guan, X. / Liu, H. / Li, N. / Zhang, B. / Yang, D. / Ma, C. / Wang, S. / Wu, D. / Ma, Y. / Fan, S. / Wang, J. / Gao, N. / Huang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5id6.cif.gz | 537.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5id6.ent.gz | 452.5 KB | Display | PDB format |
PDBx/mmJSON format | 5id6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/5id6 ftp://data.pdbj.org/pub/pdb/validation_reports/id/5id6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 144132.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A182DWE3*PLUS | ||
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#2: RNA chain | Mass: 6659.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | #4: 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: 2.76 Å3/Da / Density % sol: 55.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.16 M Magnesium acetate, 18%(w/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å |
Detector | Type: CCD pilatus CBF / Detector: CCD / Date: Jan 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→41.51 Å / Num. obs: 64262 / % possible obs: 99.6 % / Redundancy: 3.8 % / Net I/σ(I): 20.67 |
Reflection shell | Resolution: 2.38→2.42 Å |
-Processing
Software |
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Refinement | Resolution: 2.382→41.506 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.382→41.506 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 45.0357 Å / Origin y: 0.6252 Å / Origin z: 26.7772 Å
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Refinement TLS group | Selection details: all |