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- PDB-8tt9: X-ray structure of Macrophage Migration Inhibitory Factor (MIF) C... -

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Basic information

Entry
Database: PDB / ID: 8tt9
TitleX-ray structure of Macrophage Migration Inhibitory Factor (MIF) Covalently Bound to 4-hydroxyphenylpyruvate (HPP)
ComponentsMacrophage migration inhibitory factor
KeywordsCYTOKINE / MACROPHAGE MIGRATION INHIBITORY FACTOR
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 / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein homotrimerization / chemoattractant activity / 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 / DNA damage response, signal transduction by p53 class mediator / negative regulation of cell migration / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / 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 / innate immune response / negative regulation of gene expression / 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
3-(4-HYDROXY-PHENYL)PYRUVIC ACID / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.68 Å
AuthorsSchroder, G.C. / Meilleur, F. / Nix, J.C. / Crichlow, G.V. / Lolis, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: X-ray structure of Macrophage Migration Inhibitory Factor (MIF) Covalently Bound to 4-hydroxyphenylpyruvate (HPP)
Authors: Schroder, G.C. / Crichlow, G.V. / Zambrzycka, E. / Pantouris, G. / Nix, J.C. / Chayen, N. / Meilleur, F. / Lolis, E.
History
DepositionAug 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 18, 2025Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct

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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)37,7268
Polymers37,0653
Non-polymers6615
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-18 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.570, 68.870, 88.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / Details (production host): pet11b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP


Mass: 180.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M AMMONIUM SULFATE, 4% ISOPROPANOL, 0.1 M TRIS(HYDROXYMETHYL)AMINOMETHAN; MIXED WITH PROTEIN:INHIBITOR COMPLEX IN A 1:10 RATIO

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→44.22 Å / Num. obs: 48464 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 28.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.04 / Rrim(I) all: 0.085 / Net I/av σ(I): 16.1 / Net I/σ(I): 16.1
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.208 / Num. unique obs: 2461 / CC1/2: 0.314 / Rpim(I) all: 1.302 / Rrim(I) all: 2.426 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.68→44.22 Å / SU ML: 0.2211 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 20.412
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 2346 4.86 %
Rwork0.1703 45952 -
obs0.1717 48298 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.87 Å2
Refinement stepCycle: LAST / Resolution: 1.68→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 47 174 2784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01442924
X-RAY DIFFRACTIONf_angle_d1.33554034
X-RAY DIFFRACTIONf_chiral_restr0.092455
X-RAY DIFFRACTIONf_plane_restr0.0096537
X-RAY DIFFRACTIONf_dihedral_angle_d15.66251088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.3481510.34412570X-RAY DIFFRACTION97.18
1.71-1.750.35861310.32632672X-RAY DIFFRACTION99.47
1.75-1.790.32971570.28562635X-RAY DIFFRACTION99.79
1.79-1.840.27931610.25232665X-RAY DIFFRACTION99.93
1.84-1.890.27321420.21672646X-RAY DIFFRACTION99.96
1.89-1.940.25541380.2092691X-RAY DIFFRACTION100
1.94-2.010.20461240.18292681X-RAY DIFFRACTION100
2.01-2.080.21431270.18252723X-RAY DIFFRACTION100
2.08-2.160.20211350.16992706X-RAY DIFFRACTION100
2.16-2.260.22531530.17782643X-RAY DIFFRACTION99.89
2.26-2.380.22031320.18052712X-RAY DIFFRACTION99.86
2.38-2.530.22241070.18892734X-RAY DIFFRACTION99.89
2.53-2.720.24221240.18642727X-RAY DIFFRACTION99.86
2.72-2.990.20541480.18012710X-RAY DIFFRACTION100
2.99-3.430.2642960.16662794X-RAY DIFFRACTION100
3.43-4.320.14471500.12442780X-RAY DIFFRACTION99.97
4.32-44.220.1511700.1472863X-RAY DIFFRACTION99.67

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