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- PDB-6b1k: Macrophage Migration Inhibitory Factor in Complex with a Naphthyr... -

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Basic information

Entry
Database: PDB / ID: 6b1k
TitleMacrophage Migration Inhibitory Factor in Complex with a Naphthyridinone Inhibitor (3a)
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE inhibitor / CD74 BINDING / TAUTOMERASE / INHIBITOR / COMPLEX / ISOMERASE-ISOMERASE INHIBITOR COMPLEX / ISOMERASE
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 / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of macrophage activation / chemoattractant activity / protein homotrimerization / 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 / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / DNA damage response, signal transduction by p53 class mediator / 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 / 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 / cytoplasm / cytosol
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
Chem-C9G / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsKrimmer, S.G. / Robertson, M.J. / Jorgensen, W.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32136 United States
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor.
Authors: Dawson, T.K. / Dziedzic, P. / Robertson, M.J. / Cisneros, J.A. / Krimmer, S.G. / Newton, A.S. / Tirado-Rives, J. / Jorgensen, W.L.
History
DepositionSep 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,49911
Polymers37,0653
Non-polymers1,4348
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-84 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.904, 116.904, 102.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

21A-401-

HOH

31B-388-

HOH

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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 / Plasmid: PET11B / Cell (production host): BL21 / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-C9G / 2-[1-(4-hydroxyphenyl)-1H-1,2,3-triazol-4-yl]-7-methyl-1,7-naphthyridin-8(7H)-one


Mass: 319.317 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H13N5O2
#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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.1 M AMMONIUM SULFATE, 0.1 M TRIS-HCL PH 7.5, 3% ISOPROPANOL, 1.4% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.17→200 Å / Num. obs: 118139 / % possible obs: 97.9 % / Redundancy: 11.9 % / Rsym value: 0.058 / Net I/σ(I): 19.2
Reflection shellResolution: 1.17→1.23 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16818 / Rsym value: 0.727 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U18

3u18


Resolution: 1.17→82.664 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.49
RfactorNum. reflection% reflection
Rfree0.1539 5900 5 %
Rwork0.1346 --
obs0.1355 117992 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→82.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 98 333 2999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083051
X-RAY DIFFRACTIONf_angle_d0.9574225
X-RAY DIFFRACTIONf_dihedral_angle_d23.5581154
X-RAY DIFFRACTIONf_chiral_restr0.083455
X-RAY DIFFRACTIONf_plane_restr0.007652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1691-1.18240.29191800.29473430X-RAY DIFFRACTION92
1.1824-1.19630.24841940.23313674X-RAY DIFFRACTION100
1.1963-1.21090.22571950.19743716X-RAY DIFFRACTION100
1.2109-1.22630.17271960.17073708X-RAY DIFFRACTION100
1.2263-1.24240.17231950.15223711X-RAY DIFFRACTION100
1.2424-1.25940.18411950.14593710X-RAY DIFFRACTION100
1.2594-1.27740.16581960.13543716X-RAY DIFFRACTION100
1.2774-1.29650.15981950.13093720X-RAY DIFFRACTION100
1.2965-1.31670.15211950.13063697X-RAY DIFFRACTION100
1.3167-1.33830.14281960.12223721X-RAY DIFFRACTION100
1.3383-1.36140.13881960.12083728X-RAY DIFFRACTION100
1.3614-1.38620.16491960.11993715X-RAY DIFFRACTION100
1.3862-1.41280.14171960.11463726X-RAY DIFFRACTION100
1.4128-1.44170.13191950.11283705X-RAY DIFFRACTION100
1.4417-1.4730.13191960.10993736X-RAY DIFFRACTION100
1.473-1.50730.14091950.10443704X-RAY DIFFRACTION100
1.5073-1.5450.13611980.10323746X-RAY DIFFRACTION100
1.545-1.58680.13371950.10693724X-RAY DIFFRACTION100
1.5868-1.63350.12631980.10383745X-RAY DIFFRACTION100
1.6335-1.68620.13161960.10723740X-RAY DIFFRACTION100
1.6862-1.74650.12291980.11353746X-RAY DIFFRACTION100
1.7465-1.81640.1221960.11293729X-RAY DIFFRACTION100
1.8164-1.89910.13991990.11153776X-RAY DIFFRACTION100
1.8991-1.99920.12261970.11793749X-RAY DIFFRACTION100
1.9992-2.12450.13241990.11763779X-RAY DIFFRACTION100
2.1245-2.28850.1471980.12543775X-RAY DIFFRACTION100
2.2885-2.51880.15042000.13413789X-RAY DIFFRACTION100
2.5188-2.88330.17192000.14633809X-RAY DIFFRACTION100
2.8833-3.63270.16832030.14753859X-RAY DIFFRACTION100
3.6327-82.8710.17262120.15774009X-RAY DIFFRACTION100

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