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- PDB-6fvh: Macrophage Migration Inhibitory Factor (MIF) with Covalently Boun... -

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Basic information

Entry
Database: PDB / ID: 6fvh
TitleMacrophage Migration Inhibitory Factor (MIF) with Covalently Bound PITC
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / ISOMERASE INHIBITOR
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 lipopolysaccharide-mediated signaling pathway / 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 / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / prostaglandin biosynthetic process / carboxylic acid metabolic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / protein homotrimerization / positive regulation of protein kinase A signaling / 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 / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / 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
N-phenylthioformamide / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSamygina, V.R. / Bourenkov, G. / Sokolov, A.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RFBR15-54-74006 Russian Federation
CitationJournal: Biochemistry Mosc. / Year: 2018
Title: Structural Study of the Complex Formed by Ceruloplasmin and Macrophage Migration Inhibitory Factor.
Authors: Sokolov, A.V. / Dadinova, L.A. / Petoukhov, M.V. / Bourenkov, G. / Dubova, K.M. / Amarantov, S.V. / Volkov, V.V. / Kostevich, V.A. / Gorbunov, N.P. / Grudinina, N.A. / Vasilyev, V.B. / Samygina, V.R.
History
DepositionMar 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)38,05312
Polymers37,0653
Non-polymers9889
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-90 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.822, 68.375, 88.596
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: 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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-0FI / N-phenylthioformamide / PHENYL ISOTHIOCYANATE, bound form / Phenyl isothiocyanate


Mass: 137.202 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H7NS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium Sulfate, Hepes / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 80515 / % possible obs: 99.7 % / Redundancy: 12.6 % / Rpim(I) all: 0.17 / Net I/σ(I): 7.4
Reflection shellResolution: 1.4→1.42 Å / Rpim(I) all: 0.89 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FVE

6fve


Resolution: 1.4→14.97 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.64 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 4005 5.1 %RANDOM
Rwork0.13766 ---
obs0.1391 74904 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.862 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.4→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 30 451 3109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192808
X-RAY DIFFRACTIONr_bond_other_d0.0020.022571
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9833822
X-RAY DIFFRACTIONr_angle_other_deg0.99735984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61324.359117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.41815444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5971515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213075
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02552
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_it1.11.2331375
X-RAY DIFFRACTIONr_mcbond_other1.0961.2321374
X-RAY DIFFRACTIONr_mcangle_it1.3861.8551715
X-RAY DIFFRACTIONr_mcangle_other1.3871.8551716
X-RAY DIFFRACTIONr_scbond_it1.6851.5891433
X-RAY DIFFRACTIONr_scbond_other1.6421.5741421
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9472.2342086
X-RAY DIFFRACTIONr_long_range_B_refined3.38718.1483172
X-RAY DIFFRACTIONr_long_range_B_other2.56416.73046
X-RAY DIFFRACTIONr_rigid_bond_restr1.97235379
X-RAY DIFFRACTIONr_sphericity_free25.3365287
X-RAY DIFFRACTIONr_sphericity_bonded7.69655481
LS refinement shellResolution: 1.404→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 262 -
Rwork0.19 4555 -
obs--81.6 %

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