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- PDB-4eui: Crystal Structure of MIF L46F mutant -

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Basic information

Entry
Database: PDB / ID: 4eui
TitleCrystal Structure of MIF L46F mutant
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / Keto-enol tautomerase
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) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAshrafi, A. / Pojer, F. / Lashuel, H.
CitationJournal: Plos One / Year: 2012
Title: Characterization of molecular determinants of the conformational stability of macrophage migration inhibitory factor: leucine 46 hydrophobic pocket.
Authors: El-Turk, F. / Fauvet, B. / Ashrafi, A. / Ouertatani-Sakouhi, H. / Cho, M.K. / Neri, M. / Cascella, M. / Rothlisberger, U. / Pojer, F. / Zweckstetter, M. / Lashuel, H.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)37,5517
Polymers37,1673
Non-polymers3844
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-80 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.311, 88.232, 68.277
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: 12389.072 Da / Num. of mol.: 3 / Mutation: L46F
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 1.8M Ammonium sulfate in 0.1M Tris and 3% isopropanol, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 91979 / Num. obs: 87879 / % possible obs: 95.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 8.35
Reflection shellResolution: 1.7→1.77 Å / Mean I/σ(I) obs: 2.83 / % possible all: 88.04

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GD0

1gd0


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.657 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25933 2393 5.1 %RANDOM
Rwork0.22269 ---
obs0.22454 44942 97.96 %-
all-44942 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.345 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-0 Å2
2--0.17 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 20 215 2842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022686
X-RAY DIFFRACTIONr_angle_refined_deg2.1781.9583654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06224.103117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5841515
X-RAY DIFFRACTIONr_chiral_restr0.150.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212058
X-RAY DIFFRACTIONr_rigid_bond_restr8.91332686
X-RAY DIFFRACTIONr_sphericity_free13.421574
X-RAY DIFFRACTIONr_sphericity_bonded8.00152773
LS refinement shellHighest resolution: 1.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 139 -
Rwork0.349 2522 -
obs--78.61 %

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