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- PDB-3wns: Allyl isothiocyanate inhibitor complexed with Macrophage Migratio... -

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Basic information

Entry
Database: PDB / ID: 3wns
TitleAllyl isothiocyanate inhibitor complexed with Macrophage Migration Inhibitory Factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / Cytokine / Tautomerase / isomerase / Allyl 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 / 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-prop-2-en-1-ylthioformamide / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.658 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 1.2Dec 4, 2019Group: Data collection / Derived calculations / Category: reflns / reflns_shell / struct_conn
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)38,31717
Polymers37,0653
Non-polymers1,25214
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-112 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.090, 68.160, 87.370
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 , 6 types, 218 molecules

#2: Chemical ChemComp-9AI / N-prop-2-en-1-ylthioformamide


Mass: 101.170 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.73 Å3/Da / Density % sol: 55.03 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Mosaicity: 0.71 °
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 16, 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: 1.658→53.741 Å / Num. obs: 97536 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 20.99 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 6.2
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
1.658-1.753.92.150.42736370371.2430.021480.6100
1.75-1.8540.52654566560.8760.015340.9100
1.85-1.9840.82506162960.5070.8871.6100
1.98-2.1441.42335758730.2920.5112.7100
2.14-2.3441.62158954200.1980.3464100
2.34-2.6243.31958849150.1310.2335.6100
2.62-3.03461729743450.070.1269.599.8
3.03-3.713.912.21462437040.0330.05917.199.6
3.71-5.243.918.41129728870.020.03625.798.9
5.24-30.4763.719.8601116350.0180.0322.397.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.66 Å30.48 Å
Translation1.66 Å30.48 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F2K

4f2k


Resolution: 1.658→30.476 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.7488 / SU ML: 0.3 / σ(F): 0.01 / Phase error: 31.43 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.258 4711 5.07 %
Rwork0.2214 --
obs0.2232 92875 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.3 Å2 / Biso mean: 28.0055 Å2 / Biso min: 9.9 Å2
Refinement stepCycle: LAST / Resolution: 1.658→30.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 71 204 2876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072767
X-RAY DIFFRACTIONf_angle_d1.0463777
X-RAY DIFFRACTIONf_chiral_restr0.043412
X-RAY DIFFRACTIONf_plane_restr0.005493
X-RAY DIFFRACTIONf_dihedral_angle_d15.221016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.658-1.67680.38351380.362928863024100
1.6768-1.69660.4091820.373129353117100
1.6966-1.71730.43141660.375229233089100
1.7173-1.7390.39891640.36729763140100
1.739-1.76190.39771760.358929313107100
1.7619-1.7860.36641470.36129863133100
1.786-1.81150.36781260.345629463072100
1.8115-1.83860.40591820.33829623144100
1.8386-1.86730.37521920.330228303022100
1.8673-1.89790.33651740.330829543128100
1.8979-1.93060.36181380.328229613099100
1.9306-1.96570.34151310.301229653096100
1.9657-2.00350.34121260.284930213147100
2.0035-2.04440.32451830.27928843067100
2.0444-2.08880.32261500.281229593109100
2.0888-2.13740.3121680.252229653133100
2.1374-2.19090.3081910.251128933084100
2.1909-2.25010.33121560.25129453101100
2.2501-2.31630.31491330.25229573090100
2.3163-2.3910.30541770.225929103087100
2.391-2.47640.21961460.217229553101100
2.4764-2.57550.23271600.223529613121100
2.5755-2.69270.28761660.208529373103100
2.6927-2.83450.24651180.197530253143100
2.8345-3.0120.23161520.192429023054100
3.012-3.24430.20181660.181329393105100
3.2443-3.57030.17881640.165329203084100
3.5703-4.08590.17321600.15242921308199
4.0859-5.14380.19421370.14782920305799
5.1438-30.48090.20461420.19262895303798

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