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- PDB-8son: Crystal structure of macrophage migration inhibitory factor in co... -

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Basic information

Entry
Database: PDB / ID: 8son
TitleCrystal structure of macrophage migration inhibitory factor in complex with N-[3-(Trifluoromethyl)phenyl]-3-(2-chloroanilino)-2-cyano-3-thioxopropanamide
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / inhibitor / complex / ISOMERASE / ISOMERASE-ISOMERASE INHIBITOR complex
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 mature B cell apoptotic process / negative regulation of macrophage chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / carboxylic acid metabolic process / 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 B cell proliferation / positive regulation of phosphorylation / 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 / cellular senescence / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / Neutrophil degranulation / positive regulation of cell population proliferation / 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
: / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsPantouris, G. / Lolis, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the macrophage migration inhibitory factor in complex with N-[3-(Trifluoromethyl)phenyl]-3-(2-chloroanilino)-2-cyano-3-thioxopropanamide
Authors: Pantouris, G. / Lolis, E.
History
DepositionApr 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 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)38,42511
Polymers37,0653
Non-polymers1,3608
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-75 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.534, 68.827, 89.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-30Y / (2R)-3-[(2-chlorophenyl)amino]-2-cyano-3-thioxo-N-[3-(trifluoromethyl)phenyl]propanamide


Mass: 397.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H11ClF3N3OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Tris.HCl, pH 7.5, 2 M ammonium sulfate, and 3% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 53400 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.034 / Χ2: 1.701 / Net I/av σ(I): 43.058 / Net I/σ(I): 26.4 / Num. measured all: 192994
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.63-1.663.40.28426001.433199.1
1.66-1.693.50.2626341.5531100
1.69-1.723.50.2226371.5711100
1.72-1.763.50.18926581.6151100
1.76-1.793.50.16226211.6931100
1.79-1.843.60.13926351.7651100
1.84-1.883.60.11126401.8711100
1.88-1.933.60.09226391.8941100
1.93-1.993.60.07926461.9141100
1.99-2.053.60.06726651.9511100
2.05-2.133.60.05726761.9151100
2.13-2.213.70.0526611.8931100
2.21-2.313.70.04726561.8331100
2.31-2.433.70.04326671.8381100
2.43-2.593.70.0426601.8351100
2.59-2.793.70.03426991.6891100
2.79-3.073.70.0327031.6151100
3.07-3.513.70.02527181.561100
3.51-4.423.70.02127521.2841100
4.42-503.60.01928331.305197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→44.66 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19889 2709 5.1 %RANDOM
Rwork0.16972 ---
obs0.17118 50632 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.759 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.63→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 85 314 2933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022686
X-RAY DIFFRACTIONr_bond_other_d00.022472
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9853665
X-RAY DIFFRACTIONr_angle_other_deg3.7693.0065668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38624.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45215385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.385159
X-RAY DIFFRACTIONr_chiral_restr0.1660.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213082
X-RAY DIFFRACTIONr_gen_planes_other0.0280.02616
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4981.8051365
X-RAY DIFFRACTIONr_mcbond_other1.4921.8041364
X-RAY DIFFRACTIONr_mcangle_it1.9642.7071701
X-RAY DIFFRACTIONr_mcangle_other1.9642.7081702
X-RAY DIFFRACTIONr_scbond_it2.5422.0151321
X-RAY DIFFRACTIONr_scbond_other2.5412.0151322
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.552.9451964
X-RAY DIFFRACTIONr_long_range_B_refined4.99216.5153236
X-RAY DIFFRACTIONr_long_range_B_other4.61815.7523062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61210.1
12B61210.1
21A61640.1
22C61640.1
31B60780.13
32C60780.13
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 187 -
Rwork0.243 3694 -
obs--99.41 %

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