+Open data
-Basic information
Entry | Database: PDB / ID: 4p0j | ||||||
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Title | Crystal Structure of Loop-Swapped Interleukin-36Ra | ||||||
Components | Interleukin-36 receptor antagonist/Interleukin-36 gamma chimera protein | ||||||
Keywords | CYTOKINE / chimeric protein | ||||||
Function / homology | Function and homology information interleukin-1 receptor antagonist activity / Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cytokine activity ...interleukin-1 receptor antagonist activity / Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cytokine activity / cytokine-mediated signaling pathway / cell-cell signaling / cellular response to lipopolysaccharide / innate immune response / positive regulation of gene expression / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.298 Å | ||||||
Authors | Guenther, S. / Sundberg, E.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Immunol. / Year: 2014 Title: Molecular Determinants of Agonist and Antagonist Signaling through the IL-36 Receptor. Authors: Gunther, S. / Sundberg, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p0j.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p0j.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 4p0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p0j_validation.pdf.gz | 428.8 KB | Display | wwPDB validaton report |
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Full document | 4p0j_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 4p0j_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 4p0j_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/4p0j ftp://data.pdbj.org/pub/pdb/validation_reports/p0/4p0j | HTTPS FTP |
-Related structure data
Related structure data | 4izeC 4p0kC 4p0lC 1md6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16475.758 Da / Num. of mol.: 2 / Mutation: V2S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBH0, UniProt: Q9NZH8 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 1.2 M NaH2PO4, 0.6 M K2HPO4, 0.1 M CAPS, pH 10.5, 0.2 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 18, 2013 | ||||||||||||||||||||||||
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.29→29.21 Å / Num. obs: 11902 / % possible obs: 95 % / Redundancy: 1.9 % / Biso Wilson estimate: 38.46 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.083 / Net I/σ(I): 3.9 / Num. measured all: 22761 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1md6 Resolution: 2.298→29.208 Å / FOM work R set: 0.7787 / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.07 / 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 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.54 Å2 / Biso mean: 45.27 Å2 / Biso min: 22.96 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.298→29.208 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: 4
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