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Yorodumi- PDB-5o7h: Structure of the Cascade-I-Fv complex from Shewanella putrefaciens -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o7h | ||||||
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Title | Structure of the Cascade-I-Fv 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) Shewanella putrefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 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 | 5o7h.cif.gz | 308.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o7h.ent.gz | 255 KB | Display | PDB format |
PDBx/mmJSON format | 5o7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o7h_validation.pdf.gz | 490.3 KB | Display | wwPDB validaton report |
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Full document | 5o7h_full_validation.pdf.gz | 518.7 KB | Display | |
Data in XML | 5o7h_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 5o7h_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/5o7h ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o7h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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: 18863.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens (strain CN-32 / ATCC BAA-453) (bacteria) Strain: CN-32 / ATCC BAA-453 / Gene: Sputcn32_1823 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G3 | ||
#3: Protein | Mass: 35836.527 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens (strain CN-32 / ATCC BAA-453) (bacteria) Strain: CN-32 / ATCC BAA-453 / Gene: Sputcn32_1821 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G1 #4: Protein | | Mass: 38373.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella putrefaciens (strain CN-32 / ATCC BAA-453) (bacteria) Strain: CN-32 / ATCC BAA-453 / Gene: Sputcn32_1822 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G2 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 16% w/v PEG6000, 0.1 M Tris pH 8.0 and 20 mM 5-amino-2,4,6-triiodoisophthalic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.97 Å / Num. obs: 32876 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.99 / Rmerge(I) obs: 0.0547 / Net I/σ(I): 13.18 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 3271 / CC1/2: 0.72 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→49.288 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.288 Å
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Refine LS restraints |
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LS refinement shell |
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