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- PDB-8imr: Structure of ligand-free human macrophage migration inhibitory factor -
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Open data
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Basic information
Entry | Database: PDB / ID: 8imr | ||||||
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Title | Structure of ligand-free human macrophage migration inhibitory factor | ||||||
![]() | Macrophage migration inhibitory factor![]() | ||||||
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Function / homology | ![]() positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugishima, K. / Noguchi, K. / Yohda, M. / Odaka, M. / Matsumura, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of methotrexate as an inhibitor of macrophage migration inhibitory factor by high-resolution crystal structure analysis Authors: Sugishima, K. / Kariya, Y. / Ezawa, T. / Nagatoishi, S. / Tsumoto, K. / Shigeta, Y. / Noguchi, K. / Yohda, M. / Odaka, M. / Wakui, H. / Matsumura, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.2 KB | Display | ![]() |
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PDB format | ![]() | 65.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xtxC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 12355.056 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P14174, ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-EDO / ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % |
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Crystal grow![]() | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.0 M Ammonium sulfate 0.1 M Tris-HCl (pH 8.0) 4 % Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.3→50 Å / Num. obs: 95814 / % possible obs: 93.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.34 Å2 / CC1/2: 0.993 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10054 / CC1/2: 0.595 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→27.17 Å
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Refine LS restraints |
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LS refinement shell |
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