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Yorodumi- PDB-5mga: Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mga | ||||||
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Title | Structure of the Cpf1 endonuclease R-loop complex after DNA cleavage | ||||||
Components |
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Keywords | HYDROLASE / FnCpf1 / Cpf1 / R-loop / CRISPR | ||||||
Function / homology | Function and homology information Bacillus subtilis ribonuclease / : / deoxyribonuclease I / deoxyribonuclease I activity / defense response to virus / lyase activity / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. novicida U112 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Montoya, G. / Stella, S. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Nature / Year: 2017 Title: Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Authors: Stella, S. / Alcon, P. / Montoya, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mga.cif.gz | 595.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mga.ent.gz | 481.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mga_validation.pdf.gz | 479.6 KB | Display | wwPDB validaton report |
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Full document | 5mga_full_validation.pdf.gz | 520.3 KB | Display | |
Data in XML | 5mga_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 5mga_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mga ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mga | HTTPS FTP |
-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
-DNA chain , 2 types, 2 molecules CD
#3: DNA chain | Mass: 7937.139 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Francisella tularensis subsp. novicida U112 (bacteria) |
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#4: DNA chain | Mass: 3726.453 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Francisella tularensis subsp. novicida U112 (bacteria) |
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 154809.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. novicida U112 (bacteria) Gene: cpf1, FTN_1397 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0Q7Q2, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 12808.594 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Francisella tularensis subsp. novicida U112 (bacteria) |
-Non-polymers , 2 types, 132 molecules
#5: Chemical | #6: 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: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.35M sodium thiocyanate and 20.9% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→80.12 Å / Num. obs: 39708 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 65.4 Å2 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.95→2.96 Å / Redundancy: 7 % / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.35 / % possible all: 98 |
-Processing
Software |
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Refinement | Resolution: 3→39.58 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.888 / SU B: 63.13 / SU ML: 0.504 / Cross valid method: THROUGHOUT / ESU R Free: 0.459 / 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: 97.109 Å2
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Refinement step | Cycle: 1 / Resolution: 3→39.58 Å
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Refine LS restraints |
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