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- PDB-4wrb: Macrophage Migration Inhibitory Factor in complex with a biaryltr... -

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Basic information

Entry
Database: PDB / ID: 4wrb
TitleMacrophage Migration Inhibitory Factor in complex with a biaryltriazole inhibitor (3b-190)
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / CD74 binding / tautomerase / inhibitor / complex / 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 lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / 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
Chem-3TW / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.81 Å
AuthorsRobertson, M.J. / Baxter, R.H.G. / Jorgensen, W.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32136 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor.
Authors: Dziedzic, P. / Cisneros, J.A. / Robertson, M.J. / Hare, A.A. / Danford, N.E. / Baxter, R.H. / Jorgensen, W.L.
History
DepositionOct 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Data collection / Source and taxonomy
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,70519
Polymers37,0653
Non-polymers1,64016
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-99 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.294, 67.896, 89.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#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) / Cell line: Jurkat / Gene: MIF, GLIF, MMIF / Plasmid: pET11b / Details (production host): pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase

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Non-polymers , 5 types, 278 molecules

#2: Chemical ChemComp-3TW / 4-{4-[6-(2-methoxyethoxy)quinolin-2-yl]-1H-1,2,3-triazol-1-yl}phenol


Mass: 362.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18N4O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.5 % / Description: rod
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2M ammonium sulfate, 0.1M Tris-HCl pH 7, 3% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 3, 2013
RadiationMonochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→54.12 Å / Num. obs: 38289 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.2
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.99 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.81→54.12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.554 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20531 3808 10 %RANDOM
Rwork0.17391 ---
obs0.17705 34420 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--0.27 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.81→54.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 103 262 2953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192801
X-RAY DIFFRACTIONr_bond_other_d0.0010.022634
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9933812
X-RAY DIFFRACTIONr_angle_other_deg0.74336044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.95724.414111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.39715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3481513
X-RAY DIFFRACTIONr_chiral_restr0.080.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02639
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_it1.0211.781396
X-RAY DIFFRACTIONr_mcbond_other1.0211.781395
X-RAY DIFFRACTIONr_mcangle_it1.5312.6631750
X-RAY DIFFRACTIONr_mcangle_other1.5312.6631751
X-RAY DIFFRACTIONr_scbond_it1.7922.1031405
X-RAY DIFFRACTIONr_scbond_other1.7912.1051406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7833.0582060
X-RAY DIFFRACTIONr_long_range_B_refined5.17715.9133220
X-RAY DIFFRACTIONr_long_range_B_other5.04115.6233138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 260 -
Rwork0.273 2449 -
obs--97.76 %

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