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- PDB-3wnt: Multiple binding modes of benzyl isothiocyanate inhibitor complex... -

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Basic information

Entry
Database: PDB / ID: 3wnt
TitleMultiple binding modes of benzyl isothiocyanate inhibitor complexed with Macrophage Migration Inhibitory Factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / Cytokine / ISOMERASE INHIBITOR COMPLEX / Tautomerase / isomerase / Benzyl isothiocyante / 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 / phenylpyruvate tautomerase / dopachrome isomerase activity / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / dopachrome isomerase activity / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / 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
N-benzylthioformamide / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.074 Å
AuthorsSpencer, E.S. / Dale, E.J. / Gommans, A.L. / Rutledge, M.T. / 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
DepositionDec 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references

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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)38,05912
Polymers37,0653
Non-polymers9949
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-83 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.170, 68.560, 88.670
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: GLIF, MIF, MMIF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-9BE / N-benzylthioformamide


Mass: 151.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H9NS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.8 Å3/Da / Density % sol: 56 %
Description: The structure factor file contains Friedel pairs
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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Date: Aug 15, 2013 / Details: SILICON DOUBLE CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.527→54.238 Å / Num. obs: 75896 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.21 Å2 / Rsym value: 0.134 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.82-1.926.30.5420.70.542199.5
1.92-2.036.70.4530.80.453199.6
2.03-2.1770.3552.10.3551100
2.17-2.356.30.30810.308196.8
2.35-2.577.20.1754.30.1751100
2.57-2.877.20.1096.90.1091100
2.87-3.327.20.06610.70.0661100
3.32-4.066.80.0914.30.091198.8
4.06-5.756.90.03317.80.0331100
5.75-34.286.30.035110.035199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.82 Å34.28 Å
Translation1.82 Å34.28 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.074→34.28 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.28 / σ(F): 1.05 / Phase error: 26.84 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.263 2323 5.05 %
Rwork0.2218 --
obs0.2239 45965 94.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.2281 Å2
Refinement stepCycle: LAST / Resolution: 2.074→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 59 279 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082756
X-RAY DIFFRACTIONf_angle_d1.1133759
X-RAY DIFFRACTIONf_dihedral_angle_d14.171003
X-RAY DIFFRACTIONf_chiral_restr0.044407
X-RAY DIFFRACTIONf_plane_restr0.005497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0735-2.11580.27651370.23922701X-RAY DIFFRACTION100
2.1158-2.16180.28511170.2512727X-RAY DIFFRACTION100
2.1618-2.21210.3453960.312311X-RAY DIFFRACTION100
2.2121-2.26740.6628840.58081591X-RAY DIFFRACTION71
2.2674-2.32870.39471020.33451812X-RAY DIFFRACTION68
2.3287-2.39720.33671450.26232713X-RAY DIFFRACTION100
2.3972-2.47460.32261190.24912780X-RAY DIFFRACTION100
2.4746-2.5630.30331660.23722684X-RAY DIFFRACTION100
2.563-2.66560.29191550.2282720X-RAY DIFFRACTION100
2.6656-2.78680.25821400.20792723X-RAY DIFFRACTION100
2.7868-2.93370.26831200.20682733X-RAY DIFFRACTION100
2.9337-3.11740.22071730.20012726X-RAY DIFFRACTION100
3.1174-3.35790.2851410.19562669X-RAY DIFFRACTION100
3.3579-3.69540.23491460.20062711X-RAY DIFFRACTION100
3.6954-4.22930.1921800.16322628X-RAY DIFFRACTION97
4.2293-5.32530.15671630.1422700X-RAY DIFFRACTION100
5.3253-34.28460.2031390.16752713X-RAY DIFFRACTION100

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