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- PDB-5j7q: Macrophage Migration Inhibitory Factor bound to Inhibitor K664 De... -

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Basic information

Entry
Database: PDB / ID: 5j7q
TitleMacrophage Migration Inhibitory Factor bound to Inhibitor K664 Derivative
ComponentsMacrophage migration inhibitory factor
KeywordsIsomerase/Isomerase Inhibitor / Isomerase / Isomerase Inhibitor / 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 / 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
4-(imidazo[1,2-a]pyridin-2-yl)benzene-1,2-diol / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRobertson, M.J. / Jorgensen, W.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Irregularities in enzyme assays: The case of macrophage migration inhibitory factor.
Authors: Cisneros, J.A. / Robertson, M.J. / Valhondo, M. / Jorgensen, W.L.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)38,20814
Polymers37,0653
Non-polymers1,14311
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-116 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.699, 67.732, 88.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase

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Non-polymers , 5 types, 83 molecules

#2: Chemical ChemComp-6H2 / 4-(imidazo[1,2-a]pyridin-2-yl)benzene-1,2-diol


Mass: 226.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M Ammonium Sulfate, 3% isopropanol and 0.1 M Tris pH 7.0

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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: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→53.71 Å / Num. obs: 29961 / % possible obs: 98.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Χ2: 0.94 / Net I/av σ(I): 18.615 / Net I/σ(I): 6.4 / Num. measured all: 187842
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.9840.85713760.6180.4780.9830.87793.4
1.98-2.024.20.75514130.6550.4090.8610.92495.4
2.02-2.064.50.58614580.7470.3070.6630.93695.7
2.06-2.14.90.52414420.8110.2650.5890.9697.1
2.1-2.155.20.44214670.880.2150.4931.01398.4
2.15-2.25.50.41914660.8960.1960.4640.97698.1
2.2-2.255.80.35715010.9210.1620.3930.99199.1
2.25-2.316.20.34114810.9510.1490.3730.99699.3
2.31-2.3870.29114820.9670.1170.3141.03598.8
2.38-2.467.10.26214840.9690.1050.2830.99999.1
2.46-2.547.10.25215020.9770.10.2711.00599.3
2.54-2.657.10.2114990.9810.0830.2260.95199.4
2.65-2.777.10.15715050.9880.0630.170.97299.6
2.77-2.917.10.12715150.9910.0510.1370.91399.8
2.91-3.17.10.08915490.9960.0360.0960.92899.7
3.1-3.337.10.07214900.9970.0290.0780.87799.9
3.33-3.677.10.04815360.9980.0190.0520.84299.9
3.67-4.270.0415690.9990.0160.0430.85100
4.2-5.2970.03615720.9990.0150.040.853100
5.29-506.50.03616540.9990.0150.0390.93199.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U18

3u18


Resolution: 2.05→53.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.432 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2566 10 %RANDOM
Rwork0.1954 ---
obs0.1991 23028 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.01 Å2 / Biso mean: 27.31 Å2 / Biso min: 14.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 2.05→53.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 68 72 2739
Biso mean--52.85 28.88 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192831
X-RAY DIFFRACTIONr_bond_other_d0.0010.022656
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9813880
X-RAY DIFFRACTIONr_angle_other_deg0.78636099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51324.188117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85215431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6991516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02664
X-RAY DIFFRACTIONr_mcbond_it1.4822.5441425
X-RAY DIFFRACTIONr_mcbond_other1.4812.5441424
X-RAY DIFFRACTIONr_mcangle_it2.183.8071796
LS refinement shellResolution: 2.045→2.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 148 -
Rwork0.25 1378 -
all-1526 -
obs--79.65 %

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