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- PDB-7e4a: Crystal structure of MIF bound to compound 13 -

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Basic information

Entry
Database: PDB / ID: 7e4a
TitleCrystal structure of MIF bound to compound 13
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 / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid 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 / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid 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 / prostaglandin biosynthetic process / negative regulation of protein metabolic 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 tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / 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 / cytoplasm / cytosol
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
Flavoxate / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.475 Å
AuthorsFa, C.P. / Guo, D.Y. / 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 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / struct_ncs_dom_lim
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: Refinement description / Category: 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)38,26117
Polymers37,0653
Non-polymers1,19614
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-160 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.766, 68.400, 88.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 12 or resid 14...
21(chain B and (resid 1 through 12 or resid 14...
31(chain C and (resid 1 through 12 or resid 14...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 121 - 12
12VALVALALAALA(chain A and (resid 1 through 12 or resid 14...AA14 - 2714 - 27
13GLNGLNGLNGLN(chain A and (resid 1 through 12 or resid 14...AA2828
14PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
15PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
16PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
17PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
18PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
21PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 121 - 12
22VALVALSERSER(chain B and (resid 1 through 12 or resid 14...BB14 - 7614 - 76
23LYSLYSLYSLYS(chain B and (resid 1 through 12 or resid 14...BB7777
24PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
25PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
26PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
27PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
28PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
31PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 121 - 12
32VALVALALAALA(chain C and (resid 1 through 12 or resid 14...CC14 - 2714 - 27
33GLNGLNGLNGLN(chain C and (resid 1 through 12 or resid 14...CC2828
34PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
35PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
36PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
37PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
38PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114

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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.: 11 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HWL / Flavoxate / 2-piperidin-1-ylethyl 3-methyl-4-oxidanylidene-2-phenyl-chromene-8-carboxylate


Mass: 391.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.0M ammonium sulfate

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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: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.475→48.14 Å / Num. obs: 70028 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.032 / Rrim(I) all: 0.097 / Rsym value: 0.092 / Net I/av σ(I): 16.6 / Net I/σ(I): 16.6
Reflection shellResolution: 1.475→1.5 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.321 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3412 / CC1/2: 0.663 / Rpim(I) all: 0.459 / Rrim(I) all: 1.401 / Rsym value: 1.321 / % possible all: 99.3

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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: 1.475→48.14 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 1996 2.85 %
Rwork0.1756 67959 -
obs0.1765 69955 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.76 Å2 / Biso mean: 17.6746 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 1.475→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 70 411 3073
Biso mean--24.2 27.48 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162744
X-RAY DIFFRACTIONf_angle_d1.4063742
X-RAY DIFFRACTIONf_chiral_restr0.122406
X-RAY DIFFRACTIONf_plane_restr0.01489
X-RAY DIFFRACTIONf_dihedral_angle_d13.4981604
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1538X-RAY DIFFRACTION7.519TORSIONAL
12B1538X-RAY DIFFRACTION7.519TORSIONAL
13C1538X-RAY DIFFRACTION7.519TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4753-1.51220.45241390.34374776
1.5122-1.55310.37841400.28614802
1.5531-1.59880.28441440.22784799
1.5988-1.65050.29271380.20374795
1.6505-1.70940.21411450.19214801
1.7094-1.77790.24071380.17484818
1.7779-1.85880.20411460.16074816
1.8588-1.95680.22421400.17354833
1.9568-2.07940.17821440.15374833
2.0794-2.240.19791400.15044860
2.24-2.46540.18991440.16054864
2.4654-2.82210.18911420.17034890
2.8221-3.55540.1861450.17154939
3.5554-48.140.18071510.16665133

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