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Yorodumi- PDB-5o6u: Structure of the Cascade-I-Fv R-loop complex from Shewanella putr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o6u | ||||||
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Title | Structure of the Cascade-I-Fv R-loop complex from Shewanella putrefaciens | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / RNA SURVEILLANCE / ADAPTIVE IMMUNITY / CRISPR / CASCADE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella putrefaciens CN-32 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Pausch, P. / Altegoer, F. / Bange, G. | ||||||
Citation | Journal: Mol. Cell / Year: 2017 Title: Structural Variation of Type I-F CRISPR RNA Guided DNA Surveillance. Authors: Pausch, P. / Muller-Esparza, H. / Gleditzsch, D. / Altegoer, F. / Randau, L. / Bange, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o6u.cif.gz | 339.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o6u.ent.gz | 269.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/5o6u ftp://data.pdbj.org/pub/pdb/validation_reports/o6/5o6u | 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
-Uncharacterized ... , 2 types, 4 molecules CDEF
#3: Protein | Mass: 35602.055 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria) Gene: Sputcn32_1821 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G1 #4: Protein | | Mass: 37904.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria) Gene: Sputcn32_1822 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G2 |
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-DNA chain , 2 types, 2 molecules HI
#5: DNA chain | Mass: 6310.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) |
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#6: DNA chain | Mass: 8485.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) |
-RNA chain / Protein , 2 types, 2 molecules AB
#1: RNA chain | Mass: 13756.292 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Protein | Mass: 20573.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria) Gene: Sputcn32_1823 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G3 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 22.5 % w/v PEG4000, 15 % v/v glycerol, 153 mM ammonium acetate and 85 mM sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.991 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.991 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→47.66 Å / Num. obs: 32784 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.168 / Net I/σ(I): 11.66 |
Reflection shell | Resolution: 3.25→3.36 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→46.911 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→46.911 Å
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Refine LS restraints |
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LS refinement shell |
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