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- PDB-7kqx: MIF Y99C homotrimeric mutant -

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Basic information

Entry
Database: PDB / ID: 7kqx
TitleMIF Y99C homotrimeric mutant
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / MIF / mutant
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 / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid 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 / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of mature B cell apoptotic process / negative regulation of macrophage chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / carboxylic acid metabolic process / 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 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 B cell proliferation / positive regulation of phosphorylation / 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 tumor necrosis factor production / cellular senescence / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / Neutrophil degranulation / positive regulation of cell population proliferation / 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
ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsManjula, R. / Georgios, P. / Lolis, E.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Mol Biosci / Year: 2022
Title: A Cysteine Variant at an Allosteric Site Alters MIF Dynamics and Biological Function in Homo- and Heterotrimeric Assemblies.
Authors: Skeens, E. / Pantouris, G. / Shah, D. / Manjula, R. / Ombrello, M.J. / Maluf, N.K. / Bhandari, V. / Lisi, G.P. / Lolis, E.J.
History
DepositionNov 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)38,85526
Polymers36,8853
Non-polymers1,97023
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-67 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.984, 68.062, 86.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 12295.024 Da / Num. of mol.: 3 / Mutation: Y99C
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
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 3% 2-propanol, 0.1 M Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5428 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5428 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 53669 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Rrim(I) all: 0.05 / Χ2: 0.93 / Net I/σ(I): 16.3 / Num. measured all: 303731
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.633.40.33125640.8980.2040.3910.83697.9
1.63-1.663.50.32926720.8940.20.3870.86399
1.66-1.693.70.28326230.9210.1670.3310.82699.3
1.69-1.723.80.25326410.9340.1460.2930.85599.3
1.72-1.7640.22226300.8680.1260.2570.86499.7
1.76-1.84.10.19526740.9620.1070.2230.84499.7
1.8-1.854.20.15726540.9780.0850.180.86699.4
1.85-1.94.40.12326590.9850.0650.1390.89899.6
1.9-1.954.60.10626490.9880.0550.1190.89199.5
1.95-2.024.80.0926380.9910.0450.1010.90699.4
2.02-2.0950.07626820.9940.0370.0850.89499.4
2.09-2.175.20.06726590.9950.0320.0740.84299.7
2.17-2.275.60.05926980.9970.0270.0650.85499.9
2.27-2.3960.05326660.9960.0240.0580.909100
2.39-2.546.20.04827110.9980.0210.0530.838100
2.54-2.746.80.0527090.9980.020.0541.059100
2.74-3.017.80.04627180.9980.0170.051.108100
3.01-3.458.50.03827440.9990.0140.0410.974100
3.45-4.3410.10.03827630.9990.0120.041.06100
4.34-5010.60.03529150.9990.0110.0370.91100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.08 Å48.1 Å

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
SCALEPACKdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BS9

5bs9


Resolution: 1.6→48.1 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1798 2579 4.81 %
Rwork0.1528 --
obs0.1541 53581 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 125 365 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162793
X-RAY DIFFRACTIONf_angle_d1.3443789
X-RAY DIFFRACTIONf_dihedral_angle_d14.658417
X-RAY DIFFRACTIONf_chiral_restr0.095422
X-RAY DIFFRACTIONf_plane_restr0.009480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.23831380.19142720X-RAY DIFFRACTION97
1.63-1.660.23921290.1822796X-RAY DIFFRACTION99
1.66-1.70.19431330.17332800X-RAY DIFFRACTION99
1.7-1.740.23911350.17252774X-RAY DIFFRACTION100
1.74-1.780.21781300.16572834X-RAY DIFFRACTION100
1.78-1.830.19491300.16632827X-RAY DIFFRACTION100
1.83-1.880.20161810.15832778X-RAY DIFFRACTION100
1.88-1.950.18911350.15052801X-RAY DIFFRACTION99
1.95-2.010.17811440.14642790X-RAY DIFFRACTION99
2.02-2.10.18331500.1482808X-RAY DIFFRACTION99
2.1-2.190.18421220.15282863X-RAY DIFFRACTION100
2.19-2.310.19681730.14952803X-RAY DIFFRACTION100
2.31-2.450.16821440.14352849X-RAY DIFFRACTION100
2.45-2.640.20351610.15932821X-RAY DIFFRACTION100
2.64-2.910.19651420.1492862X-RAY DIFFRACTION100
2.91-3.330.16231330.14752909X-RAY DIFFRACTION100
3.33-4.190.13641370.12862919X-RAY DIFFRACTION100
4.19-48.10.16321620.16753048X-RAY DIFFRACTION100

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