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- PDB-8htw: Crystal Structure of the ring nuclease Sso2081 Y133F mutant from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8htw | ||||||
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Title | Crystal Structure of the ring nuclease Sso2081 Y133F mutant from Saccharolobus solfataricus in its apo form | ||||||
![]() | CRISPR system ring nuclease SSO2081 | ||||||
![]() | HYDROLASE / Sso2081 / ring nuclease / mutant / Y133F | ||||||
Function / homology | CRISPR-assoc protein, NE0113/Csx13 / CRISPR-associated protein NE0113 (Cas_NE0113) / Restriction endonuclease type II-like / Lyases; Phosphorus-oxygen lyases / defense response to virus / lyase activity / cytoplasm / CRISPR system ring nuclease SSO2081![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, Z. / Du, L. / Luo, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of stepwise cyclic tetra-adenylate cleavage by the type III CRISPR ring nuclease Crn1/Sso2081. Authors: Du, L. / Zhang, D. / Luo, Z. / Lin, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.3 KB | Display | ![]() |
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PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.2 KB | Display | ![]() |
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Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yghC ![]() 7yglC ![]() 7yhlSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20538.842 Da / Num. of mol.: 2 / Mutation: Y133F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO2081 / Production host: ![]() ![]() References: UniProt: Q7LYJ6, Lyases; Phosphorus-oxygen lyases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 24137 / % possible obs: 97.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 1.183 / Num. unique obs: 1778 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7YHL Resolution: 2→47.626 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.784 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.185 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.345 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.626 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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