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- PDB-3jtu: Crystal structure of macrophage migration inhibitory factor (mif)... -

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Basic information

Entry
Database: PDB / ID: 3jtu
TitleCrystal structure of macrophage migration inhibitory factor (mif) with hydroxyquinoline inhibitor 708 at 1.86a resolution
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / PROTEIN-LIGAND COMPLEX / CYTOKINE / CYTOPLASM / IMMUNE RESPONSE / INFLAMMATORY RESPONSE / INNATE IMMUNITY / SECRETED / Phosphoprotein
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 / chemoattractant activity / positive regulation of cAMP/PKA signal transduction / protein homotrimerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of cellular senescence / 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 MAP kinase activity / positive regulation of cytokine production / cytokine activity / 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 / 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) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7-(pyridin-2-ylmethyl)quinolin-8-ol / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsMclean, L. / Zhang, Y.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Discovery of covalent inhibitors for MIF tautomerase via cocrystal structures with phantom hits from virtual screening.
Authors: McLean, L.R. / Zhang, Y. / Li, H. / Li, Z. / Lukasczyk, U. / Choi, Y.M. / Han, Z. / Prisco, J. / Fordham, J. / Tsay, J.T. / Reiling, S. / Vaz, R.J. / Li, Y.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)41,1808
Polymers40,2793
Non-polymers9015
Water4,558253
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-59 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.494, 67.431, 88.740
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 / Phenylpyruvate tautomerase / L-dopachrome tautomerase / L-dopachrome isomerase / ...MIF / Phenylpyruvate tautomerase / L-dopachrome tautomerase / L-dopachrome isomerase / Glycosylation-inhibiting factor / GIF


Mass: 13426.209 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLIF, MIF, MMIF / Plasmid: PET22B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-ZIN / 7-(pyridin-2-ylmethyl)quinolin-8-ol


Mass: 236.269 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H12N2O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5 M AMMONIUM SULFATE, 2 mM EDTA, 0.1 M HEPES, PH 6.5, VAPOR DIFFUSION/HANGING DROP, , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 15, 2008 / Details: XENOCS FOX 2D
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 34676 / % possible obs: 98.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.059 / Χ2: 1.013 / Net I/σ(I): 27.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.927.30.13428811.10482.3
1.92-1.997.50.11434741.083100
1.99-2.087.60.09534551.072100
2.08-2.197.60.08434881.031100
2.19-2.337.70.07735211.02100
2.33-2.517.80.07134980.97100
2.51-2.767.80.06634910.919100
2.76-3.167.90.0635561100
3.16-3.997.80.05435910.913100
3.99-1007.40.04437211.04899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→23.85 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 248648 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1700 4.9 %RANDOM
Rwork0.177 ---
obs0.178 34349 99 %-
all-34618 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.736 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 65.14 Å2 / Biso mean: 18.964 Å2 / Biso min: 9.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.86→23.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 64 253 2979
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.482
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.222 247 4.9 %
Rwork0.185 4815 -
all-5062 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION44708_ADDUCT.PAR4708_ADDUCT.TOP

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