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Yorodumi- PDB-1uiz: Crystal Structure Of Macrophage Migration Inhibitory Factor From ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uiz | ||||||
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Title | Crystal Structure Of Macrophage Migration Inhibitory Factor From Xenopus Laevis. | ||||||
Components | Macrophage Migration Inhibitory Factor | ||||||
Keywords | CYTOKINE / Tautomerase / Macrophage Migration Inhibitory Factor / MIF | ||||||
Function / homology | Function and homology information phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine activity / inflammatory response / innate immune response / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Suzuki, M. / Takamura, Y. / Maeno, M. / Tochinai, S. / Iyaguchi, D. / Tanaka, I. / Nishihira, J. / Ishibashi, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Xenopus laevis Macrophage Migration Inhibitory Factor Is Essential for Axis Formation and Neural Development. Authors: Suzuki, M. / Takamura, Y. / Maeno, M. / Tochinai, S. / Iyaguchi, D. / Tanaka, I. / Nishihira, J. / Ishibashi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uiz.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uiz.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 1uiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uiz_validation.pdf.gz | 374.3 KB | Display | wwPDB validaton report |
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Full document | 1uiz_full_validation.pdf.gz | 387.5 KB | Display | |
Data in XML | 1uiz_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1uiz_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/1uiz ftp://data.pdbj.org/pub/pdb/validation_reports/ui/1uiz | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 assembly is a trimer generated from chain A, B and C. Chain D generates a trimer by the operations: -y, x-y, z and -x+y, -x, z. |
-Components
#1: Protein | Mass: 12511.357 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 38603569, UniProt: Q76BK2*PLUS #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: 1.98 Å3/Da / Density % sol: 37.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-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: Apr 13, 2003 |
Radiation | Monochromator: Confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 13284 / Num. obs: 12890 / % possible obs: 97.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 52.9 Å2 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 49.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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