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Yorodumi- PDB-3dji: Crystal Structure of Macrophage Migration Inhibitory Factor Bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dji | ||||||
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Title | Crystal Structure of Macrophage Migration Inhibitory Factor Bound to an Acetaminophen Dimer Derived from NAPQI | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | ISOMERASE / homotrimer / acetaminophen dimer / Cytokine / Inflammatory response / Phosphoprotein | ||||||
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: 1.95 Å | ||||||
Authors | Crichlow, G.V. / Lolis, E. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and kinetic analyses of macrophage migration inhibitory factor active site interactions. Authors: Crichlow, G.V. / Lubetsky, J.B. / Leng, L. / Bucala, R. / 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 | 3dji.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dji.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 3dji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/3dji ftp://data.pdbj.org/pub/pdb/validation_reports/dj/3dji | HTTPS FTP |
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-Related structure data
Related structure data | 3ce4C 3djhSC 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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2 |
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Unit cell |
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Details | The biological unit is possibly a trimer. There are two trimers per asymmetric unit. |
-Components
#1: Protein | Mass: 12355.056 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14174, phenylpyruvate tautomerase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-3E1 / | #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: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 M Ammonium sulfate, 3% Isopropanol, 0.1 M Tris(hydroxymethyl)aminomethane, mixed with protein-inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 94 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: May 2, 2008 / Details: Mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→90 Å / Num. obs: 47844 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Χ2: 1.307 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.443 / Num. unique all: 4773 / Χ2: 0.926 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DJH Resolution: 1.95→77.68 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.832 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 51.808 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.65 Å2 / Biso mean: 32.06 Å2 / Biso min: 15.42 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→77.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.021
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Xplor file |
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