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- PDB-3smb: Phenethylisothiocyanate Covalently Bound to Macrophage Migration ... -

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Basic information

Entry
Database: PDB / ID: 3smb
TitlePhenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (MIF)
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / cytokine / receptor binding / secreted / 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-phenylethyl)thioformamide / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsCrichlow, G.V. / Lolis, E.J.
CitationJournal: Biochemistry / Year: 2012
Title: Structural interactions dictate the kinetics of macrophage migration inhibitory factor inhibition by different cancer-preventive isothiocyanates.
Authors: Crichlow, G.V. / Fan, C. / Keeler, C. / Hodsdon, M. / Lolis, E.J.
History
DepositionJun 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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

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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)37,94918
Polymers37,0653
Non-polymers88415
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-145 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.492, 67.670, 87.771
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 / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-LE2 / N-(2-phenylethyl)thioformamide / Phenylethyl isothiocyanate, bound form / N-(2-phenylethyl)thiocarbamyl group / Phenethyl isothiocyanate


Mass: 165.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11NS
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STARTING MATERIAL IS PHENETHYL ISOTHIOCYANATE. IT BINDS COVALENTLY TO PRO 1. LE2 CORRESPONDS TO ...THE STARTING MATERIAL IS PHENETHYL ISOTHIOCYANATE. IT BINDS COVALENTLY TO PRO 1. LE2 CORRESPONDS TO THE FINAL PRODUCT.

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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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 3% isopropanol, 0.1 M tris(hydroxymethyl)aminomethane; mixed with protein:inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 10, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 52662 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Χ2: 1.565 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.6-1.634.30.2774.1326140.84998.8
1.63-1.664.50.24826360.8699.1
1.66-1.694.50.22226140.88499.1
1.69-1.724.50.2426101.17599.1
1.72-1.764.50.1926471.02399.1
1.76-1.84.50.15926570.94199.5
1.8-1.854.50.14626531.03999.9
1.85-1.94.60.13126641.25199.8
1.9-1.954.50.13826461.64999.9
1.95-2.024.60.11126781.49199.7
2.02-2.094.70.10526571.5299.8
2.09-2.174.60.10126721.72999.7
2.17-2.274.70.09926731.9299.3
2.27-2.394.70.09626461.86799.4
2.39-2.544.60.09126812.0799.5
2.54-2.743.90.08626312.07796.8
2.74-3.014.20.07826732.23298.7
3.01-3.454.30.06826742.22698.2
3.45-4.343.30.06124292.66587.8
4.34-1003.90.05225072.56286.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.374 / Cor.coef. Fo:Fc: 0.647 / Cor.coef. Io to Ic: 0.606
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DJH

3djh


Resolution: 1.6→100 Å / Occupancy max: 1 / Occupancy min: 0.24 / Isotropic thermal model: isotropic, restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1074 -random
Rwork0.181 ---
all-52638 --
obs-52568 97.8 %-
Displacement parametersBiso max: 61.2 Å2 / Biso mean: 19.52 Å2 / Biso min: 11.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 45 434 3055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.288 173 -
Rwork0.255 --
obs-8707 98.7 %

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