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

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Basic information

Entry
Database: PDB / ID: 3wnr
TitleMultiple binding modes of benzyl isothiocyanate inhibitor complexed with Macrophage Migration Inhibitory Factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / Cytokine / Tautomerase / isomerae / 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 / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis ...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 / positive regulation of arachidonate secretion / cytokine receptor binding / 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 lipopolysaccharide-mediated signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / 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 / protein homotrimerization / chemoattractant activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cAMP/PKA signal transduction / negative regulation of cellular senescence / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / DNA damage response, signal transduction by p53 class mediator / 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 tumor necrosis factor production / cellular senescence / protease binding / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / innate immune response / negative regulation of gene expression / 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 / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.008 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
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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)38,49517
Polymers37,0653
Non-polymers1,43014
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-97 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.480, 68.640, 86.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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, 306 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.13 %
Description: The structure factor file contains Friedel pairs
Mosaicity: 0.32 °
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: Apr 2, 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: 2.008→43.235 Å / Num. obs: 55686 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.37 Å2 / Rsym value: 0.123 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.01-2.126.80.4191.82672039540.1710.4194.599.5
2.12-2.257.40.3432.22783737870.1340.3435.999.7
2.25-2.47.40.2742.82632435740.1070.2747.399.9
2.4-2.597.40.2383.22468833320.0920.2388.7100
2.59-2.847.40.1664.62290030900.0650.16612.1100
2.84-3.177.40.1116.92075027900.0430.11116.9100
3.17-3.677.40.07110.41860625030.0280.07124.1100
3.67-4.497.40.05313.51575521300.0210.05331.7100
4.49-6.357.30.05412.31218716780.0210.05428.8100
6.35-43.2356.70.04314.5671310050.0180.04327.899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.7 Å43.23 Å
Translation6.7 Å43.23 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.12data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F2K

4f2k


Resolution: 2.008→43.235 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.8876 / SU ML: 0.19 / σ(F): 1.31 / Phase error: 18.6 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2001 2652 5.06 %
Rwork0.1498 --
obs0.1524 52457 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.15 Å2 / Biso mean: 17.6658 Å2 / Biso min: 5.78 Å2
Refinement stepCycle: LAST / Resolution: 2.008→43.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 86 292 2979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082780
X-RAY DIFFRACTIONf_angle_d1.0163789
X-RAY DIFFRACTIONf_chiral_restr0.046410
X-RAY DIFFRACTIONf_plane_restr0.005494
X-RAY DIFFRACTIONf_dihedral_angle_d14.4431021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.008-2.04450.28451160.21382634275099
2.0445-2.08390.24281120.182623273599
2.0839-2.12640.21811310.165126382769100
2.1264-2.17260.24061570.16752553271099
2.1726-2.22320.20051210.1626542775100
2.2232-2.27880.21261580.160626302788100
2.2788-2.34040.19451240.151525982722100
2.3404-2.40920.22191440.158826372781100
2.4092-2.4870.20731300.16226382768100
2.487-2.57590.22631280.161626282756100
2.5759-2.6790.24271470.148725962743100
2.679-2.80090.19121360.153726402776100
2.8009-2.94850.23921520.148926542806100
2.9485-3.13320.19911730.140625702743100
3.1332-3.37510.17811520.146626042756100
3.3751-3.71450.17571440.122126352779100
3.7145-4.25160.13691420.117326442786100
4.2516-5.3550.17581540.131525992753100
5.355-43.2450.22611310.180626302761100

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