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- PDB-8q3j: Crystal structure of mIL-38 in complex with a neutralizing Fab e0... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8q3j | ||||||
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Title | Crystal structure of mIL-38 in complex with a neutralizing Fab e04 fragment | ||||||
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![]() | CYTOKINE / IL-38 / Fab / anti-tumor Immunity / Neutralizing antibody / Chemotherapy | ||||||
Function / homology | ![]() Interleukin-38 signaling / Interleukin-36 pathway / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / endoplasmic reticulum-Golgi intermediate compartment / cytokine activity / cytokine-mediated signaling pathway / cellular response to lipopolysaccharide / positive regulation of gene expression / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garcia-Pardo, J. / Da Silva, P. / Mora, J. / Wiechmann, S. / Putyrski, M. / You, X. / Kannt, A. / Ernst, A. / Brune, B. / Weigert, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Neutralizing IL-38 activates gammaDelta T cell-dependent anti-tumor immunity and sensitizes for chemotherapy Authors: Da Silva, P. / Mora, J. / Wiechmann, S. / Putyrski, M. / Garcia-Pardo, J. / You, X. / Kannt, A. / Ernst, A. / Brune, B. / Weigert, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 269 KB | Display | ![]() |
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PDB format | ![]() | 184.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Unit cell |
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Components
#1: Protein | Mass: 17095.502 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 24599.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 25652.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-PO4 / #5: 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: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / Details: 27.5% (w/v) PEG 1500 100 mM SPG buffer, pH 8.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→70.11 Å / Num. obs: 50677 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 55.59 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.41 |
Reflection shell | Resolution: 2.35→2.49 Å / Num. unique obs: 8129 / CC1/2: 0.99 / % possible all: 99.2 |
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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: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→70.11 Å
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Refine LS restraints |
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LS refinement shell |
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