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Yorodumi- PDB-3ijg: Macrophage Migration Inhibitory Factor (MIF) Bound to the (R)-Ste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ijg | ||||||
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Title | Macrophage Migration Inhibitory Factor (MIF) Bound to the (R)-Stereoisomer of AV1013 | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | ISOMERASE / allosteric binding / Cytokine / Immune response / Inflammatory response / Innate immunity / Phosphoprotein / Secreted | ||||||
Function / homology | Function and homology information positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / prostaglandin biosynthetic process / carboxylic acid metabolic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / protein homotrimerization / positive regulation of protein kinase A signaling / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of cellular senescence / DNA damage response, signal transduction by p53 class mediator / positive regulation of B cell proliferation / positive regulation of phosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Crichlow, G.V. / Cho, Y. / Lolis, E.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Allosteric inhibition of macrophage migration inhibitory factor revealed by ibudilast. Authors: Cho, Y. / Crichlow, G.V. / Vermeire, J.J. / Leng, L. / Du, X. / Hodsdon, M.E. / Bucala, R. / Cappello, M. / Gross, M. / Gaeta, F. / Johnson, K. / Lolis, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ijg.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ijg.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ijg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/3ijg ftp://data.pdbj.org/pub/pdb/validation_reports/ij/3ijg | HTTPS FTP |
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-Related structure data
Related structure data | 3ijjC 3djhS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12355.056 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLIF, MIF, MMIF / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-AVR / ( | #4: 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: 2.68 Å3/Da / Density % sol: 54.13 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 M ammonium sulfate, 3% isopropanol, 0.5 M NaCl, 0.1 M tris(hydroxymethyl)aminomethane; mixed with protein:inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2009 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 42688 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.073 / Χ2: 1.333 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.514 / Num. unique all: 2099 / Χ2: 0.838 / % possible all: 96 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.335 / Cor.coef. Fo:Fc: 0.724 / Cor.coef. Io to Ic: 0.691
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DJH Resolution: 1.7→100 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.894 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 65.071 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.14 Å2 / Biso mean: 22.329 Å2 / Biso min: 10.86 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å / Rfactor Rfree error: 0.073
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Xplor file |
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