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Yorodumi- PDB-6thh: Crystal structure of type I-D CRISPR-Cas nuclease Cas10d in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6thh | |||||||||
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Title | Crystal structure of type I-D CRISPR-Cas nuclease Cas10d in complex with the SIRV3 AcrID1 (gp02) anti-CRISPR protein | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / CRISPR / Cas / type I-D / Cas10 / Cas10d / complex / anti-CRISPR | |||||||||
Function / homology | Sulfolobus islandicus filamentous virus, Orf14 / Protein of unknown function (DUF1374) / PHOSPHATE ION / MafI family immunity protein / CRISPR-associated protein, CscA Function and homology information | |||||||||
Biological species | Sulfolobus islandicus rudivirus 3 Sulfolobus islandicus LAL14/1 (acidophilic) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.48 Å | |||||||||
Authors | Manav, M.C. / Brodersen, D.E. | |||||||||
Funding support | Denmark, 2items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for inhibition of an archaeal CRISPR-Cas type I-D large subunit by an anti-CRISPR protein. Authors: Manav, M.C. / Van, L.B. / Lin, J. / Fuglsang, A. / Peng, X. / Brodersen, D.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6thh.cif.gz | 213.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6thh.ent.gz | 176.2 KB | Display | PDB format |
PDBx/mmJSON format | 6thh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6thh_validation.pdf.gz | 520.2 KB | Display | wwPDB validaton report |
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Full document | 6thh_full_validation.pdf.gz | 528.7 KB | Display | |
Data in XML | 6thh_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 6thh_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/6thh ftp://data.pdbj.org/pub/pdb/validation_reports/th/6thh | 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: Protein | Mass: 13086.693 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus rudivirus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B3SN05 #2: Protein | | Mass: 98332.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus islandicus LAL14/1 (acidophilic) Gene: SiL_0609 / Production host: Escherichia coli (E. coli) / References: UniProt: M9U4Y8 #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-ZN / | Has ligand of interest | Y | |
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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: 3.37 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Hepes 7.5, 2% (w/v) PEG 8000, 5% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.48→67.542 Å / Num. obs: 21713 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 137.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.48→3.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2139 / CC1/2: 0.6 / % possible all: 99.8 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.48→67.542 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.77 / 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: 282.81 Å2 / Biso mean: 137.0532 Å2 / Biso min: 61.23 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.48→67.542 Å
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LS refinement shell |
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