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Yorodumi- PDB-4gru: crystallographic and biological characterization of N- and C- ter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gru | ||||||
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Title | crystallographic and biological characterization of N- and C- terminus mutants of human MIF | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | cytokine / ISOMERASE / alpha/beta mixture | ||||||
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 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 / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of mature B cell apoptotic process / negative regulation of macrophage chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / carboxylic acid metabolic process / prostaglandin biosynthetic process / negative regulation of protein metabolic 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 tumor necrosis factor production / cellular senescence / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / Neutrophil degranulation / positive regulation of cell population proliferation / 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 / Resolution: 1.92 Å | ||||||
Authors | Fan, C. / Lolis, E. | ||||||
Citation | Journal: To be Published Title: crystallographic and biological characterization of N- and C- terminus mutants of human MIF Authors: Fan, C. / Lolis, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gru.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gru.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 4gru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/4gru ftp://data.pdbj.org/pub/pdb/validation_reports/gr/4gru | HTTPS FTP |
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-Related 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 / Mutation: Pro1-Ala2 are insertions Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: 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 | #4: Chemical | #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: 3.69 Å3/Da / Density % sol: 66.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.0M ammonium sulfate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2010 |
Radiation | Monochromator: graphte / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. all: 42406 / Num. obs: 42321 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 22.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: human MIF Resolution: 1.92→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.23 Å / Luzzati sigma a obs: 0.15 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→50 Å
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Refine LS restraints |
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