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Yorodumi- PDB-4xx8: Crystal structure of Pro1 deletion mutant of human macrophage mig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xx8 | ||||||
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Title | Crystal structure of Pro1 deletion mutant of human macrophage migration inhibitory factor | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | ISOMERASE / surface / mutation | ||||||
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 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 / 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 phosphorylation / positive regulation of B cell proliferation / 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 / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Pantouris, G. / Lolis, E. | ||||||
Citation | Journal: Chem.Biol. / Year: 2015 Title: An Analysis of MIF Structural Features that Control Functional Activation of CD74. Authors: Pantouris, G. / Syed, M.A. / Fan, C. / Rajasekaran, D. / Cho, T.Y. / Rosenberg, E.M. / Bucala, R. / Bhandari, V. / 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 | 4xx8.cif.gz | 83.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xx8.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 4xx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xx8_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 4xx8_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 4xx8_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 4xx8_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/4xx8 ftp://data.pdbj.org/pub/pdb/validation_reports/xx/4xx8 | HTTPS FTP |
-Related structure data
Related structure data | 4p01C 4p0hC 4pkzC 4pluC 4trfC 4truC 4xx7C 5bs9C 5bscC 5bsiC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 114 / Label seq-ID: 1 - 113
NCS ensembles :
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-Components
#1: Protein | Mass: 12257.941 Da / Num. of mol.: 3 / Mutation: Pro1 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli (E. coli) References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 2.74 Å3/Da / Density % sol: 55.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 M ammonium Sulphate, 3% 2-propanol, 20 mM Tris.HCl, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 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 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 40049 / % possible obs: 99.9 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.286 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DJH Resolution: 1.77→48.17 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.663 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→48.17 Å
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Refine LS restraints |
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