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Yorodumi- PDB-4f2k: Macrophage Migration Inhibitory Factor covalently complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f2k | ||||||
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Title | Macrophage Migration Inhibitory Factor covalently complexed with phenethylisothiocyanate | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / cytokine / Tautomerase / Phenethylisothiocyanate / ISOMERASE / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
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 / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / prostaglandin biosynthetic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / 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 / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / protease binding / secretory granule lumen / 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: 1.53 Å | ||||||
Authors | Tyndall, J.D.A. / Bernhagen, J. / Hampton, M.B. / Wilbanks, S.M. / Rutledge, M.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Macrophage migration inhibitory factor covalently complexed with phenethyl isothiocyanate Authors: Tyndall, J.D.A. / Lue, H. / Rutledge, M.T. / Bernhagen, J. / Hampton, M.B. / Wilbanks, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f2k.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f2k.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 4f2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/4f2k ftp://data.pdbj.org/pub/pdb/validation_reports/f2/4f2k | HTTPS FTP |
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-Related structure data
Related structure data | 3l5vS 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: pETllb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-IPA / #5: 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: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.9M (NH4)2SO4, 100mM Tris pH 8.0, 200mM NaCl, 4% v/v isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 13, 2011 / Details: Osmic VariMax |
Radiation | Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→31.64 Å / Num. all: 63013 / Num. obs: 51308 / % possible obs: 81.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.31 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6220 / % possible all: 14 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L5V Resolution: 1.53→31.64 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.572 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.53 Å2 / Biso mean: 18.5078 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→31.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.527→1.567 Å / Total num. of bins used: 20
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