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

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Basic information

Entry
Database: PDB / ID: 3jsg
TitleCrystal structure of macrophage migration inhibitory factor (mif) with hydroxyquinoline inhibitor 707 at 1.58a resolution
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / protein-ligand complex / Cytokine / Cytoplasm / Immune response / Inflammatory response / Innate immunity / Phosphoprotein / Secreted
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 / cytokine receptor binding / positive regulation of arachidonate secretion / positive regulation of lipopolysaccharide-mediated signaling pathway / 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 / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of arachidonate secretion / positive regulation of lipopolysaccharide-mediated signaling pathway / 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 / negative regulation of protein metabolic process / prostaglandin biosynthetic 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 peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / 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-3-ylmethyl)quinolin-8-ol / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 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 10, 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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)41,2769
Polymers40,2793
Non-polymers9976
Water4,432246
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-65 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.493, 67.616, 88.886
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-0IN / 7-(pyridin-3-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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
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, TEMPERATURE 298.0K , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 56125 / % possible obs: 97.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.072 / Χ2: 1.288 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.58-1.644.70.4444650.45979.9
1.64-1.74.90.35657030.523100
1.7-1.784.80.28556560.605100
1.78-1.874.90.21356790.79399.9
1.87-1.994.90.15656491.12100
1.99-2.144.90.11857131.316100
2.14-2.364.90.09157141.43100
2.36-2.74.90.07657591.493100
2.7-3.44.80.0658262.024100
3.4-504.50.05559612.95198.7

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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
Starting model: PDB entry 1GCZ

1gcz


Resolution: 1.58→31.55 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 338064 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2737 5 %RANDOM
Rwork0.188 ---
obs0.188 54392 96.4 %-
all-56064 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.288 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 72.42 Å2 / Biso mean: 22.693 Å2 / Biso min: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2---1.86 Å20 Å2
3---1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.58→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 69 246 2977
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 1.58→1.68 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 409 4.9 %
Rwork0.227 7920 -
all-8329 -
obs--89.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION54707_adduct.par4707_adduct.top

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