+Open data
-Basic information
Entry | Database: PDB / ID: 1wu3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of recombinant murine interferon beta | |||||||||
Components | Interferon betaInterferon type I | |||||||||
Keywords | CYTOKINE / alpha-helix-bundle | |||||||||
Function / homology | Function and homology information negative regulation of Lewy body formation / B cell activation involved in immune response / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / chloramphenicol O-acetyltransferase activity / Interferon alpha/beta signaling / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production ...negative regulation of Lewy body formation / B cell activation involved in immune response / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / chloramphenicol O-acetyltransferase activity / Interferon alpha/beta signaling / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / cytokine receptor binding / macrophage activation involved in immune response / cellular response to dsRNA / negative regulation of viral genome replication / response to exogenous dsRNA / type I interferon-mediated signaling pathway / B cell proliferation / negative regulation of osteoclast differentiation / cell surface receptor signaling pathway via JAK-STAT / humoral immune response / cellular response to interferon-beta / positive regulation of autophagy / positive regulation of apoptotic signaling pathway / cellular response to dexamethasone stimulus / B cell differentiation / cytokine activity / cellular response to virus / neuron cellular homeostasis / cytokine-mediated signaling pathway / defense response to virus / adaptive immune response / defense response to bacterium / innate immune response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å | |||||||||
Authors | Senda, T. / Saitoh, S. / Mitsui, Y. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Refined crystal structure of recombinant murine interferon-beta at 2.15 A resolution Authors: Senda, T. / Saitoh, S. / Mitsui, Y. #1: Journal: Embo J. / Year: 1992 Title: Three-dimensional crystal structure of recombinant murine interferon-beta Authors: Senda, T. / Shimazu, T. / Matsuda, S. / Kawano, G. / Shimizu, H. / Nakamura, K.T. / Mitsui, Y. #2: Journal: Proc.Jpn.Acad.,Ser.B / Year: 1990 Title: Three-dimensional structure of recombinant murine interferon-beta Authors: Senda, T. / Matsuda, S. / Kurihara, H. / Nakamura, K.T. / Kawano, G. / Shimizu, H. / Mizuno, H. / Mitsui, Y. #3: Journal: Pharmacol.Ther. / Year: 1993 Title: Structural, functional and evolutionary implications of the three-dimensional crystal structure of murine interferon-beta Authors: Mitsui, Y. / Senda, T. / Shimazu, T. / Matsuda, S. / Utsumi, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wu3.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wu3.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/1wu3 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/1wu3 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19760.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01575 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 59 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: Ammonium Sulfate, dioxane, acetate buffer, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04 Å |
---|---|
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 7, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. all: 22157 / Num. obs: 14666 / % possible obs: 66.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.18 % / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.8→1.88 Å / % possible all: 12.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.15→7.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.918 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.203 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.011 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→7.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.202 Å / Total num. of bins used: 20
|