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- PDB-4osf: 4-(2-isothiocyanatoethyl)phenol inhibitor complexed with Macropha... -

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Basic information

Entry
Database: PDB / ID: 4osf
Title4-(2-isothiocyanatoethyl)phenol inhibitor complexed with Macrophage Migration Inhibitory Factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / Cytokine / Tautomerase / isomerase / Benzyl isothiocyante / 4-(2-isothiocyanatoethyl)phenol / 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 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 DNA damage response, signal transduction by p53 class mediator / negative regulation of cellular senescence / 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-[2-(4-hydroxyphenyl)ethyl]thioformamide / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsSpencer, E.S. / Dale, E.J. / Gommans, A.L. / Vo, C.T. / Rutledge, M.T. / Nakatani, Y. / Gamble, A.B. / Smith, R.A.J. / Wilbanks, S.M. / Hampton, M.B. / Tyndall, J.D.A.
CitationJournal: Eur.J.Med.Chem. / Year: 2015
Title: Multiple binding modes of isothiocyanates that inhibit macrophage migration inhibitory factor
Authors: Spencer, E.S. / Dale, E.J. / Gommans, A.L. / Rutledge, M.T. / Vo, C.T. / Nakatani, Y. / Gamble, A.B. / Smith, R.A. / Wilbanks, S.M. / Hampton, M.B. / Tyndall, J.D.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Nov 8, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)38,89321
Polymers37,0653
Non-polymers1,82818
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-187 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.060, 96.060, 103.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: GLIF, MIF, MMIF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase

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Non-polymers , 5 types, 240 molecules

#2: Chemical ChemComp-4MT / N-[2-(4-hydroxyphenyl)ethyl]thioformamide / N-(4-hydroxyphenethyl)methanethioamide


Mass: 181.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11NOS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.74 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.9M ammonium sulfate, 100mM Tris pH 8.0, 200mM NaCl, 4%(v/v) 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 18, 2013 / Details: Osmic VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→30.1 Å / Num. obs: 62538 / Biso Wilson estimate: 23.11 Å2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F2K

4f2k


Resolution: 1.62→30.096 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 3141 5.03 %
Rwork0.1973 --
obs0.1986 62505 88.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.5859 Å2
Refinement stepCycle: LAST / Resolution: 1.62→30.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 102 222 2925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072812
X-RAY DIFFRACTIONf_angle_d1.0363845
X-RAY DIFFRACTIONf_dihedral_angle_d16.771025
X-RAY DIFFRACTIONf_chiral_restr0.047418
X-RAY DIFFRACTIONf_plane_restr0.006498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.64530.37581160.37592057217368
1.6453-1.67230.35671460.35362613275987
1.6723-1.70110.34161490.33272872302195
1.7011-1.73210.33191740.30472969314398
1.7321-1.76540.31021650.28023009317499
1.7654-1.80140.29221680.255430063174100
1.8014-1.84060.28931790.244130113190100
1.8406-1.88340.30671480.243330393187100
1.8834-1.93050.5819320.435968671868
1.9305-1.98270.23251090.20371820192966
1.9827-2.0410.21591570.185730663223100
2.041-2.10690.24631000.20152230233073
2.1069-2.18210.21421330.18330963229100
2.1821-2.26950.30041120.26162127223991
2.2695-2.37270.22431560.18772965312199
2.3727-2.49780.2361700.185130333203100
2.4978-2.65420.19251490.182630973246100
2.6542-2.85890.21691210.18082744286589
2.8589-3.14640.18951830.176430673250100
3.1464-3.6010.19821480.1732864301293
3.601-4.53440.17561640.162735289988
4.5344-30.10140.20691620.188632583420100

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