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Open data
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Basic information
Entry | Database: PDB / ID: 8kbf | ||||||
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Title | Structure of CbTad1 complexed with 1',3'-cADPR and cA3 | ||||||
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![]() | VIRAL PROTEIN | ||||||
Function / homology | nucleotide binding / Chem-OJC / RNA / Thoeris anti-defense 1![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiao, Y. / Feng, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of CbTad1 complexed with 1',3'-cADPR and cA3 Authors: Xiao, Y. / Feng, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 52.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uawS S: Starting model for refinement |
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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: 15862.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: RNA chain | Mass: 942.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 3.2 M Ammonium sulfate, 0.1 M Citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→35.8 Å / Num. obs: 15435 / % possible obs: 100 % / Redundancy: 40 % / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.021 / Rrim(I) all: 0.136 / Χ2: 0.99 / Net I/σ(I): 22 / Num. measured all: 617623 |
Reflection shell | Resolution: 2.31→2.37 Å / % possible obs: 100 % / Redundancy: 41.1 % / Rmerge(I) obs: 2.305 / Num. measured all: 45768 / Num. unique obs: 1113 / CC1/2: 0.768 / Rpim(I) all: 0.363 / Rrim(I) all: 2.334 / Χ2: 0.94 / Net I/σ(I) obs: 2.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7uaw Resolution: 2.31→35.8 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.47 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→35.8 Å
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Refine LS restraints |
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LS refinement shell |
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