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- PDB-4oyq: (6-isothiocyanatohexyl)benzene inhibitor complexed with Macrophag... -

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Basic information

Entry
Database: PDB / ID: 4oyq
Title(6-isothiocyanatohexyl)benzene inhibitor complexed with Macrophage Migration Inhibitory Factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / Tautomerase / isomerase / Cytokine / 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 arachidonate secretion / positive regulation of lipopolysaccharide-mediated signaling pathway / 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 arachidonate secretion / positive regulation of lipopolysaccharide-mediated signaling pathway / 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
6-isothiocyanatohexylbenzene / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
University of Otago New Zealand
CitationJournal: To be published
Title: To be published
Authors: Spencer, 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.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Data collection / Other
Revision 1.2Aug 6, 2014Group: Database references / Structure summary
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_site / symmetry
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_site.details / _symmetry.Int_Tables_number

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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)38,29212
Polymers37,0653
Non-polymers1,2269
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-80 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.690, 67.690, 88.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) / Strain (production host): BL21(DE3)
References: UniProt: P14174, phenylpyruvate tautomerase, phenylpyruvate tautomerase
#2: Chemical ChemComp-1X2 / 6-isothiocyanatohexylbenzene


Mass: 219.346 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H17NS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.9 M ammonium sulfate, 100 mM Tris pH 8.0, 200 mM NaCl, 4%(v/v) 2-propanol

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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 / Detector: CCD / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→37.12 Å / Num. obs: 45634 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 11.97 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.8
Reflection shellHighest resolution: 1.79 Å / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F2K

4f2k


Resolution: 1.7→33.845 Å / FOM work R set: 0.899 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.57 / Phase error: 17.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 4355 5.02 %
Rwork0.1738 82322 -
obs0.1748 86677 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.43 Å2 / Biso mean: 14.16 Å2 / Biso min: 4.47 Å2
Refinement stepCycle: final / Resolution: 1.7→33.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 32 151 2784
Biso mean--35.13 21.26 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072833
X-RAY DIFFRACTIONf_angle_d1.1023883
X-RAY DIFFRACTIONf_chiral_restr0.045428
X-RAY DIFFRACTIONf_plane_restr0.006507
X-RAY DIFFRACTIONf_dihedral_angle_d15.0181065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.71930.25011440.226327792923
1.7193-1.73960.21471600.210127942954
1.7396-1.76080.22831150.202126752790
1.7608-1.78310.20871390.186827922931
1.7831-1.80650.23021430.193427292872
1.8065-1.83130.18921310.1827712902
1.8313-1.85740.23021430.178127092852
1.8574-1.88520.19771370.170827862923
1.8852-1.91460.2761590.190227252884
1.9146-1.9460.18771650.179327102875
1.946-1.97960.18611300.175427822912
1.9796-2.01550.19511390.164827362875
2.0155-2.05430.21411450.174427102855
2.0543-2.09620.23471430.177627442887
2.0962-2.14180.20261620.163427652927
2.1418-2.19160.17651600.165927412901
2.1916-2.24640.19731330.173427382871
2.2464-2.30710.21871500.164926952845
2.3071-2.3750.15361600.169527842944
2.375-2.45170.1691190.173527282847
2.4517-2.53930.21521680.181327402908
2.5393-2.64090.18171520.180527312883
2.6409-2.7610.22661630.179327102873
2.761-2.90650.20651280.180327602888
2.9065-3.08850.21231880.183327592947
3.0885-3.32680.21161180.189827182836
3.3268-3.66120.1471280.158827702898
3.6612-4.19020.13281380.148827662904
4.1902-5.27590.17911500.146827342884
5.2759-33.85160.19751450.185927412886
Refinement TLS params.Method: refined / Origin x: 22.0233 Å / Origin y: 7.3099 Å / Origin z: 12.1219 Å
111213212223313233
T0.055 Å2-0.0036 Å2-0.0024 Å2-0.0571 Å20.0095 Å2--0.0581 Å2
L0.8876 °20.0523 °20.181 °2-0.9691 °2-0.2409 °2--0.7192 °2
S0.0151 Å °0.0103 Å °-0.0438 Å °0.0042 Å °0.0374 Å °0.089 Å °0.0426 Å °-0.0402 Å °-0.0453 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 115
2X-RAY DIFFRACTION1allB1 - 115
3X-RAY DIFFRACTION1allC1 - 115
4X-RAY DIFFRACTION1allD1 - 152
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allF1 - 2

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