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- PDB-8imr: Structure of ligand-free human macrophage migration inhibitory factor -

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Basic information

Entry
Database: PDB / ID: 8imr
TitleStructure of ligand-free human macrophage migration inhibitory factor
ComponentsMacrophage migration inhibitory factor
KeywordsCYTOKINE
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 / dopachrome isomerase activity / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / dopachrome isomerase activity / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / negative regulation of protein metabolic process / prostaglandin biosynthetic 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 peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / protease binding / secretory granule lumen / 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
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSugishima, K. / Noguchi, K. / Yohda, M. / Odaka, M. / Matsumura, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K07011 Japan
CitationJournal: To Be Published
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
DepositionMar 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,81014
Polymers37,0653
Non-polymers74511
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-44 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.745, 68.471, 88.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Macrophage migration inhibitory factor / MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / ...MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase


Mass: 12355.056 Da / Num. of mol.: 3
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 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→27.17 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.356 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2169 4937 5.16 %
Rwork0.1953 90756 -
obs0.1964 95693 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.61 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 46 290 2937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052855
X-RAY DIFFRACTIONf_angle_d0.73653901
X-RAY DIFFRACTIONf_chiral_restr0.0843428
X-RAY DIFFRACTIONf_plane_restr0.0056519
X-RAY DIFFRACTIONf_dihedral_angle_d4.75361987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.36551900.3543087X-RAY DIFFRACTION97.36
1.31-1.330.26841870.26163173X-RAY DIFFRACTION99.67
1.33-1.350.24511670.24973163X-RAY DIFFRACTION99.73
1.35-1.360.2561470.23693242X-RAY DIFFRACTION99.88
1.36-1.380.23981660.23363191X-RAY DIFFRACTION99.88
1.38-1.40.23641880.23163168X-RAY DIFFRACTION100
1.4-1.420.24751870.21993174X-RAY DIFFRACTION99.82
1.42-1.440.29181860.24613192X-RAY DIFFRACTION99.88
1.44-1.460.291820.25053165X-RAY DIFFRACTION99.94
1.46-1.490.29521710.27853219X-RAY DIFFRACTION99.74
1.49-1.510.23311740.20933161X-RAY DIFFRACTION99.85
1.51-1.540.20221310.20023268X-RAY DIFFRACTION99.88
1.54-1.570.19911630.19123181X-RAY DIFFRACTION99.97
1.57-1.60.21381690.18033230X-RAY DIFFRACTION99.97
1.6-1.640.21941660.18143218X-RAY DIFFRACTION99.91
1.64-1.680.20681840.18063208X-RAY DIFFRACTION100
1.68-1.720.19551750.1833206X-RAY DIFFRACTION100
1.72-1.760.19551560.18633209X-RAY DIFFRACTION100
1.76-1.820.22441840.18433226X-RAY DIFFRACTION100
1.82-1.870.17681690.18753213X-RAY DIFFRACTION99.97
1.87-1.940.2803670.26291615X-RAY DIFFRACTION49.38
1.94-2.020.19741940.18573191X-RAY DIFFRACTION98.89
2.02-2.110.20171890.17843221X-RAY DIFFRACTION100
2.11-2.220.21961490.17952758X-RAY DIFFRACTION85.6
2.22-2.360.1991780.18211461X-RAY DIFFRACTION45.78
2.36-2.540.22871930.18973254X-RAY DIFFRACTION99.97
2.54-2.80.2211700.19483275X-RAY DIFFRACTION99.97
2.8-3.20.21871850.19053298X-RAY DIFFRACTION100
3.2-4.030.2244750.17761349X-RAY DIFFRACTION40.65
4.03-27.170.18191950.17513440X-RAY DIFFRACTION99.56

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