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- PDB-8qjk: Structure of the cytoplasmic domain of csx23 from Vibrio cholera ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qjk | ||||||
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Title | Structure of the cytoplasmic domain of csx23 from Vibrio cholera in complex with cyclic tetra-adenylate (cA4) | ||||||
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![]() | GENE REGULATION / DNA BINDING PROTEIN Type III CRISPR effector cA4 EPR | ||||||
Function / homology | : / ACETYL GROUP / RNA![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McMahon, S.A. / McQuarrie, S. / Gloster, T.M. / Gruschow, S. / White, M.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A cyclic-nucleotide binding membrane protein provides CRISPR-mediated antiphage defence in Vibrio cholera Authors: McMahon, S.A. / McQuarrie, S. / Gloster, T.M. / White, M.F. / Gruschow, S. / Ackermann, K. / Bode, B.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.4 KB | Display | ![]() |
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PDB format | ![]() | 21.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 453.5 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10399.886 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: 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 | ||||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #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 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2MLiS04, 0.1M NaAcetate, 42.5% peg400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 18, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→46.97 Å / Num. obs: 5251 / % possible obs: 89.1 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.76→1.91 Å / Num. unique obs: 264 / CC1/2: 0.721 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 41.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.761→46.97 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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