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Yorodumi- PDB-2gdg: Crystal structure of covalently modified macrophage inhibitory factor -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gdg | ||||||
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Title | Crystal structure of covalently modified macrophage inhibitory factor | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | ISOMERASE / Pro-1 pucker | ||||||
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 / Cell surface interactions at the vascular wall / phenylpyruvate tautomerase / L-dopachrome isomerase / positive regulation of adaptive immune response / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / Cell surface interactions at the vascular wall / phenylpyruvate tautomerase / L-dopachrome isomerase / positive regulation of adaptive immune response / 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 macrophage chemotaxis / negative regulation of mature B cell apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / 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 / Neutrophil degranulation / cytokine activity / positive regulation of MAP kinase activity / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / myelin sheath / regulation of cell population proliferation / protease binding / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / positive regulation of protein phosphorylation / negative regulation of gene expression / innate immune response / protein-containing complex binding / negative regulation of apoptotic process / cell surface / extracellular space / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Golubkov, P.A. / Hackert, M.L. | ||||||
Citation | Journal: Bioorg.Chem. / Year: 2006 Title: Inactivation of the phenylpyruvate tautomerase activity of macrophage migration inhibitory factor by 2-oxo-4-phenyl-3-butynoate. Authors: Golubkov, P.A. / Johnson Jr., W.H. / Czerwinski, R.M. / Person, M.D. / Wang, S.C. / Whitman, C.P. / Hackert, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gdg.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gdg.ent.gz | 129.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gdg_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 2gdg_full_validation.pdf.gz | 526.9 KB | Display | |
Data in XML | 2gdg_validation.xml.gz | 30 KB | Display | |
Data in CIF | 2gdg_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/2gdg ftp://data.pdbj.org/pub/pdb/validation_reports/gd/2gdg | HTTPS FTP |
-Related structure data
Related structure data | 1mffS 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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Details | The biological assembly is a trimer of the asymmetric unit. |
-Components
#1: Protein | Mass: 12383.024 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mif / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS / References: UniProt: P34884, phenylpyruvate tautomerase #2: 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: 3.05 Å3/Da / Density % sol: 59.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 8000, 0.05M sodium phosphate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 23, 2002 |
Radiation | Monochromator: bent cylindrical Si-mirror (Rh coating); Si(111) double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 78970 / Num. obs: 76879 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 1.45→1.5 Å / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MFF Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.017 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Ambiguous inhibitor density; inhibitor coordinates not included.
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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: 22.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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