+Open data
-Basic information
Entry | Database: PDB / ID: 7xcb | ||||||
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Title | Crystal structure of the mouse interleukin-9 | ||||||
Components | Interleukin-9Interleukin 9 | ||||||
Keywords | CYTOKINE / interleukin / type I cytokine | ||||||
Function / homology | Function and homology information interleukin-9 receptor binding / Interleukin-9 signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / B cell proliferation / immunoglobulin mediated immune response / regulation of peptidyl-tyrosine phosphorylation / B cell differentiation / cytokine activity ...interleukin-9 receptor binding / Interleukin-9 signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / B cell proliferation / immunoglobulin mediated immune response / regulation of peptidyl-tyrosine phosphorylation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of cell growth / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Kim, J.W. / Lee, J.-O. / Park, S.M. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the mouse interleukin-9 Authors: Kim, J.W. / Lee, J.-O. / Park, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xcb.cif.gz | 38.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xcb.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 7xcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/7xcb ftp://data.pdbj.org/pub/pdb/validation_reports/xc/7xcb | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13428.491 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: High five insect cells / Gene: Il9 / Plasmid: pFastBac1-HM / Cell line (production host): High five insect cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15247 | ||
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#2: Sugar | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.18 Å3/Da / Density % sol: 76.26 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1M citric acid(pH 3.5), 2.0M Ammonium sulfate / PH range: 3.5-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2021 |
Radiation | Monochromator: DCM Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→30 Å / Num. obs: 4255 / % possible obs: 99.7 % / Redundancy: 19.82 % / CC1/2: 0.85 / Rrim(I) all: 0.062 / Net I/σ(I): 41.13 |
Reflection shell | Resolution: 3.4→3.49 Å / Redundancy: 18.55 % / Num. unique obs: 297 / CC1/2: 0.783 / Rrim(I) all: 0.228 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AF-P15247-F1 Resolution: 3.4→27.57 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 123.74 Å2 / Biso min: 38.06 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→27.57 Å
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LS refinement shell | Resolution: 3.4→4.28 Å /
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