+Open data
-Basic information
Entry | Database: PDB / ID: 4xfs | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of IL-18 SER Mutant I | ||||||||||||
Components | Interleukin-18 | ||||||||||||
Keywords | CYTOKINE / Interleukin-18 / IL-18 / immune defense / surface entropy reduction | ||||||||||||
Function / homology | Function and homology information interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / neutrophil activation / positive regulation of interleukin-13 production / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway ...interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / neutrophil activation / positive regulation of interleukin-13 production / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / sleep / Interleukin-1 processing / positive regulation of NK T cell proliferation / triglyceride homeostasis / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / natural killer cell mediated cytotoxicity / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / establishment of skin barrier / Pyroptosis / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of smooth muscle cell proliferation / cholesterol homeostasis / cytokine activity / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / inflammatory response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||||||||
Authors | Krumm, B.E. / Meng, X. / Xiang, Y. / Deng, J. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Crystallization of interleukin-18 for structure-based inhibitor design. Authors: Krumm, B. / Meng, X. / Xiang, Y. / Deng, J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xfs.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xfs.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xfs_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4xfs_full_validation.pdf.gz | 458.5 KB | Display | |
Data in XML | 4xfs_validation.xml.gz | 15 KB | Display | |
Data in CIF | 4xfs_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/4xfs ftp://data.pdbj.org/pub/pdb/validation_reports/xf/4xfs | HTTPS FTP |
-Related structure data
Related structure data | 4xftC 4xfuC 3f62S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
3 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 155 / Label seq-ID: 1 - 155
|
-Components
#1: Protein | Mass: 17965.373 Da / Num. of mol.: 2 / Mutation: K139A, K140A, E141A, E143A, L144A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL18, IGIF, IL1F4 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q14116 #2: Chemical | ChemComp-DMS / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.7 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 47% PEG 2K MME, 0.1M HEPES, 5% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 18429 / % possible obs: 94.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 31.1 Å2 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / % possible all: 81.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3F62 Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.077 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.818 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|