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- PDB-8q44: Crystal structure of cA4-bound Can2 (E364R) in complex with oligo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q44 | ||||||
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Title | Crystal structure of cA4-bound Can2 (E364R) in complex with oligo-T DNA | ||||||
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![]() | DNA BINDING PROTEIN / Can2 / cyclic oligoadenylates / cA4 / CARF / CRISPR ancillary nuclease | ||||||
Function / homology | tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / metal ion binding / : / : / DNA / RNA / DUF1887 family protein![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jungfer, K. / Sigg, A. / Jinek, M. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2. Authors: Jungfer, K. / Sigg, A. / Jinek, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 425 KB | Display | ![]() |
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PDB format | ![]() | 307.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 47.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8q3yC ![]() 8q3zC ![]() 8q40C ![]() 8q41C ![]() 8q42C ![]() 8q43C 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: 51227.375 Da / Num. of mol.: 2 / Mutation: E364R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Thebr_0943 / Production host: ![]() ![]() #2: DNA chain | | Mass: 867.621 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() #3: RNA chain | | Type: Polycyclic / Class: Antiviral / Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Cyclic oligoadenylates such as c-tetraAMP were found to be novel bacterial second messengers. Antiviral in context of signalling for Type III CRISPR-Cas systems. Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002431 #4: Chemical | ChemComp-MN / #5: Water | ChemComp-HOH / | Compound details | CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic ...CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic oligoadenylate signaling was found to be essential for the type III system against the jumbo phage. | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.61 % / Description: plate-shaped crystals |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM Tris pH 8, 17.1% (v/v) PEG 550 MME, 4.3% (w/v) PEG 2000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57.46 Å / Num. obs: 37158 / % possible obs: 99.03 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07879 / Rpim(I) all: 0.03259 / Rrim(I) all: 0.0854 / Net I/σ(I): 13.22 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.7711 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 3660 / CC1/2: 0.854 / Rpim(I) all: 0.3141 / Rrim(I) all: 0.8338 / % possible all: 98.62 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→57.46 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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