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- PDB-7e45: Crystal structure of compound 7 bound to MIF -

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Basic information

Entry
Database: PDB / ID: 7.0E+45
TitleCrystal structure of compound 7 bound to MIF
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / tautomease 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-HWO / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.433 Å
AuthorsFan, C.P. / Yang, L.
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)38,13717
Polymers37,0653
Non-polymers1,07114
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-175 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.315, 67.914, 86.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HWO / (2R)-7-[(2R,3R,4R,5S,6S)-6-(hydroxymethyl)-3-[(2R,3R,4R,5R,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-(4-methoxy-3-oxidanyl-phenyl)-5-oxidanyl-2,3-dihydrochromen-4-one


Mass: 610.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H34O15
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M ammonium sulfate, 0.1 M Tris pH 7.0, 3% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.43→47.81 Å / Num. obs: 73421 / % possible obs: 99.8 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Rsym value: 0.067 / Net I/σ(I): 20
Reflection shellResolution: 1.43→1.46 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.165 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3456 / CC1/2: 0.788 / Rpim(I) all: 0.511 / Rrim(I) all: 1.223 / Rsym value: 1.165 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIF

1mif


Resolution: 1.433→47.81 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 3479 4.74 %
Rwork0.1611 69869 -
obs0.1623 73348 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.49 Å2 / Biso mean: 20.3304 Å2 / Biso min: 8.39 Å2
Refinement stepCycle: final / Resolution: 1.433→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 56 410 3048
Biso mean--33.22 29.69 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112703
X-RAY DIFFRACTIONf_angle_d1.2683690
X-RAY DIFFRACTIONf_chiral_restr0.123414
X-RAY DIFFRACTIONf_plane_restr0.008480
X-RAY DIFFRACTIONf_dihedral_angle_d9.471357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.433-1.45240.4411420.372263296
1.4524-1.47310.3571260.31892791100
1.4731-1.49510.34861550.28642746100
1.4951-1.51850.351330.29672767100
1.5185-1.54340.33681470.26352777100
1.5434-1.570.19481270.18252750100
1.57-1.59850.23371610.18192736100
1.5985-1.62930.21591460.16222773100
1.6293-1.66260.18161530.14132760100
1.6626-1.69870.19351610.14172732100
1.6987-1.73820.22031450.13982802100
1.7382-1.78170.17991270.13172782100
1.7817-1.82990.19161460.13232780100
1.8299-1.88370.1477930.1252821100
1.8837-1.94450.19421100.16382808100
1.9445-2.0140.18471490.13452785100
2.014-2.09470.15591430.15232794100
2.0947-2.190.18341430.13682802100
2.19-2.30540.17131340.15312787100
2.3054-2.44990.15011510.1472816100
2.4499-2.6390.20551170.16732846100
2.639-2.90460.19361380.17452842100
2.9046-3.32480.18521450.16262842100
3.3248-4.18850.14161330.1422890100
4.1885-47.810.1611540.16263008100

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