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- PDB-7e47: Crystal structure of compound 6 bound to MIF -

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Basic information

Entry
Database: PDB / ID: 7.0E+47
TitleCrystal structure of compound 6 bound to MIF
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / tautomerase and cytokine
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 / dopachrome isomerase activity / phenylpyruvate tautomerase / 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 / dopachrome isomerase activity / phenylpyruvate tautomerase / 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
Chem-HWR / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsFan, C.P. / Yang, L. / Guo, D.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570762 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Identification and Structure-Activity Relationships of Dietary Flavonoids as Human Macrophage Migration Inhibitory Factor (MIF) Inhibitors.
Authors: Yang, L. / Guo, D. / Fan, C.
History
DepositionFeb 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,89611
Polymers37,0653
Non-polymers8318
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-112 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.388, 67.713, 88.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HWR / (2S,3R,4R,5R,6R)-2-[(2S,3R,4S,5R,6S)-6-(hydroxymethyl)-2-[[(2R,4R)-2-(4-hydroxyphenyl)-4,5-bis(oxidanyl)-3,4-dihydro-2H-chromen-7-yl]oxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-6-methyl-oxane-3,4,5-triol


Mass: 582.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34O14 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.0M ammonium sulfate, 3% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.376→44.112 Å / Num. obs: 84320 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 16.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.019 / Rrim(I) all: 0.062 / Rsym value: 0.059 / Net I/σ(I): 22.8
Reflection shellResolution: 1.38→1.4 Å / Rmerge(I) obs: 1.528 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4052 / CC1/2: 0.63 / Rpim(I) all: 0.498 / Rrim(I) all: 1.609 / Rsym value: 1.528 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIF

1mif


Resolution: 1.38→44.11 Å / SU ML: 0.1649 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.9069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1793 1999 2.37 %
Rwork0.1541 82195 -
obs0.1547 84194 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 1.38→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 48 348 2997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152727
X-RAY DIFFRACTIONf_angle_d1.34583722
X-RAY DIFFRACTIONf_chiral_restr0.181419
X-RAY DIFFRACTIONf_plane_restr0.0103485
X-RAY DIFFRACTIONf_dihedral_angle_d6.7277381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.31151430.27125740X-RAY DIFFRACTION98.82
1.41-1.450.30571430.23655796X-RAY DIFFRACTION100
1.45-1.490.26561410.21925805X-RAY DIFFRACTION99.88
1.49-1.540.23741370.20115828X-RAY DIFFRACTION99.8
1.54-1.590.20541450.15595804X-RAY DIFFRACTION100
1.59-1.660.19551410.14335847X-RAY DIFFRACTION99.97
1.66-1.730.17141430.14135861X-RAY DIFFRACTION100
1.73-1.820.18911460.13475830X-RAY DIFFRACTION100
1.82-1.940.17331410.145835X-RAY DIFFRACTION99.68
1.94-2.090.15191410.13365854X-RAY DIFFRACTION99.85
2.09-2.30.19341410.13635882X-RAY DIFFRACTION99.78
2.3-2.630.16961400.15225933X-RAY DIFFRACTION99.98
2.63-3.310.18731460.16095982X-RAY DIFFRACTION100
3.32-44.110.14961510.14966198X-RAY DIFFRACTION99.76

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