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- PDB-4z15: MIF in complex with 3-(2-furylmethyl)-2-thioxo-1,3-thiazolan-4-one -

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Basic information

Entry
Database: PDB / ID: 4z15
TitleMIF in complex with 3-(2-furylmethyl)-2-thioxo-1,3-thiazolan-4-one
ComponentsMacrophage migration inhibitory factor
KeywordsIsomerase/Isomerase Inhibitor / covalent inhibitor / protein surface modification / 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 / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis ...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 arachidonate secretion / cytokine receptor binding / 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 lipopolysaccharide-mediated signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of macrophage activation / chemoattractant activity / protein homotrimerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cAMP/PKA signal transduction / negative regulation of cellular senescence / 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 / DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / cellular senescence / protease binding / secretory granule lumen / 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 / 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) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCho, T.Y.
CitationJournal: J. Cell. Mol. Med. / Year: 2017
Title: Structural basis for decreased induction of class IB PI3-kinases expression by MIF inhibitors.
Authors: Singh, A.K. / Pantouris, G. / Borosch, S. / Rojanasthien, S. / Cho, T.Y.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)37,8317
Polymers37,4833
Non-polymers3484
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-62 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.680, 68.060, 88.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 12494.230 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe polypeptide, Macrophage migration inhibitory factor, with PRO at the N-terminus was incubated ...The polypeptide, Macrophage migration inhibitory factor, with PRO at the N-terminus was incubated with 3-(2-furylmethyl)-2-thioxo-1,3-thiazolan-4-one to produce the modified N-terminal residue (4N8)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris, ammonium sulfate, isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.6→26.95 Å / Num. obs: 54348 / % possible obs: 98.8 % / Redundancy: 6.4 % / Rsym value: 0.062 / Net I/σ(I): 6.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIF

1mif


Resolution: 1.6→26.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.355 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21016 2734 5.1 %RANDOM
Rwork0.17809 ---
obs0.17975 50956 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.485 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 19 276 2859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192644
X-RAY DIFFRACTIONr_bond_other_d0.0010.022418
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.9843604
X-RAY DIFFRACTIONr_angle_other_deg0.96535552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39924.51102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9271510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213066
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02606
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_it1.7411.7761366
X-RAY DIFFRACTIONr_mcbond_other1.7421.7771365
X-RAY DIFFRACTIONr_mcangle_it2.2882.6711695
X-RAY DIFFRACTIONr_mcangle_other2.2872.6711696
X-RAY DIFFRACTIONr_scbond_it2.9982.0371278
X-RAY DIFFRACTIONr_scbond_other2.9122.011267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.082.9171890
X-RAY DIFFRACTIONr_long_range_B_refined5.41816.1023073
X-RAY DIFFRACTIONr_long_range_B_other5.2815.5522935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 192 -
Rwork0.21 3665 -
obs--97.6 %

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