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- PDB-6b2c: Macrophage Migration Inhibitory Factor in Complex with a Naphthyr... -

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Basic information

Entry
Database: PDB / ID: 6b2c
TitleMacrophage Migration Inhibitory Factor in Complex with a Naphthyridinone Inhibitor (4b)
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 myeloid leukocyte cytokine production involved in immune response / negative regulation of myeloid cell apoptotic process / phenylpyruvate tautomerase / L-dopachrome isomerase / regulation of macrophage activation / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of mature B cell apoptotic process ...: / positive regulation of myeloid leukocyte cytokine production involved in immune response / negative regulation of myeloid cell apoptotic process / phenylpyruvate tautomerase / L-dopachrome isomerase / regulation of macrophage activation / dopachrome isomerase activity / phenylpyruvate tautomerase activity / cytokine receptor binding / negative regulation of mature B cell apoptotic process / negative regulation of macrophage chemotaxis / carboxylic acid metabolic process / positive regulation of arachidonate secretion / positive regulation of lipopolysaccharide-mediated signaling pathway / prostaglandin biosynthetic process / negative regulation of protein metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of cellular senescence / positive regulation of cAMP/PKA signal transduction / 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 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 fibroblast proliferation / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / positive regulation of tumor necrosis factor production / 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 / negative regulation of apoptotic process / Neutrophil degranulation / cell surface / : / extracellular exosome / extracellular region / 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
Chem-C9Y / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 19, 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)37,5435
Polymers37,0653
Non-polymers4772
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-47 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.425, 97.425, 105.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-C9Y / {2-[1-(3-fluoro-4-hydroxyphenyl)-1H-1,2,3-triazol-4-yl]-8-oxo-1,7-naphthyridin-7(8H)-yl}acetic acid


Mass: 381.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12FN5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.99 Å3/Da / Density % sol: 68.49 %
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, 2% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→200 Å / Num. obs: 38918 / % possible obs: 98.1 % / Redundancy: 4 % / Rsym value: 0.077 / Net I/σ(I): 9
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5897 / Rsym value: 0.422 / % possible all: 93.1

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Processing

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

3u18


Resolution: 2→65.922 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.08
RfactorNum. reflection% reflection
Rfree0.2216 1946 5 %
Rwork0.1914 --
obs0.1929 38915 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→65.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 31 143 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082677
X-RAY DIFFRACTIONf_angle_d0.7623660
X-RAY DIFFRACTIONf_dihedral_angle_d13.9071582
X-RAY DIFFRACTIONf_chiral_restr0.063405
X-RAY DIFFRACTIONf_plane_restr0.006482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9995-2.04950.31121180.26182250X-RAY DIFFRACTION84
2.0495-2.10490.26921390.22512634X-RAY DIFFRACTION100
2.1049-2.16680.24061410.21582675X-RAY DIFFRACTION100
2.1668-2.23680.2741390.20312652X-RAY DIFFRACTION100
2.2368-2.31670.23551400.20792663X-RAY DIFFRACTION100
2.3167-2.40950.23331400.17842649X-RAY DIFFRACTION100
2.4095-2.51910.19711400.18442661X-RAY DIFFRACTION99
2.5191-2.65190.27541400.20352665X-RAY DIFFRACTION100
2.6519-2.81810.24541400.20342654X-RAY DIFFRACTION99
2.8181-3.03570.2661400.21152674X-RAY DIFFRACTION99
3.0357-3.34120.24461410.2142663X-RAY DIFFRACTION99
3.3412-3.82460.21921400.18352670X-RAY DIFFRACTION99
3.8246-4.81840.17061410.15972675X-RAY DIFFRACTION97
4.8184-65.95820.19871470.18682784X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4535-0.59320.64160.7299-0.53010.3921-0.2321-0.1736-0.04670.12920.1685-0.0661-0.20030.0329-0.24370.2087-0.25670.03790.4001-0.01760.3012-22.932338.36278.0573
20.1995-0.17510.02270.41130.12890.2094-0.1253-0.96990.13510.5764-0.40860.68360.4289-0.4373-0.0080.3778-0.0671-0.02840.4931-0.13120.4235-36.206845.715313.4887
30.45970.15710.03321.01740.3720.697-0.0914-0.2416-0.2873-0.07830.0788-0.1498-0.01960.38310.00920.3327-0.1630.0680.3529-0.02950.3711-19.801735.2803-1.4011
40.35350.05420.29970.2309-0.26920.4033-0.1154-0.01570.0762-0.26710.00250.1032-0.5120.0082-0.01590.3727-0.1505-0.01860.3342-0.03030.3501-27.858547.39631.6953
50.2385-0.18360.09930.1802-0.21050.4266-0.25460.1790.2084-0.25070.0807-0.2357-0.46040.2103-0.01540.4149-0.21790.05890.35970.00630.3296-17.45944.4041-0.6615
60.3226-0.087-0.05910.22390.26121.2336-0.1443-0.23190.1648-0.1247-0.10150.1186-0.2193-0.5959-0.04020.3517-0.1377-0.01920.4034-0.05310.4424-43.46738.26432.9211
70.73040.02310.4150.03620.10680.5308-0.06270.1653-0.0761-0.1280.2421-0.3748-0.22610.332300.375-0.10320.0580.3214-0.04610.366-22.424725.7898-10.4922
80.63190.55480.0330.53520.1870.3917-0.32910.5645-0.438-0.34990.0889-0.4252-0.13740.71610.03810.6159-0.32970.18020.5516-0.04440.3927-18.726535.787-17.2061
90.91150.4969-0.68430.2716-0.41811.06010.1906-0.2202-0.9295-0.3425-0.2575-0.46990.6330.1323-0.04910.4595-0.0824-0.00090.2397-0.00990.4014-29.01618.4574-7.192
100.940.08020.78570.29560.12240.6132-0.10950.3225-0.2789-0.28210.22070.1901-0.24530.38470.00630.5289-0.15860.07360.3732-0.05310.2955-29.473228.5194-18.9287
110.83980.0538-0.30270.0003-0.00720.5535-0.4609-0.0782-0.0079-0.39410.18630.2164-0.18930.117-0.20910.5402-0.251-0.05490.26320.02270.2618-30.388144.2406-9.9703
120.7185-0.1578-0.30440.46380.10260.11820.15240.1521-0.156-0.0191-0.0179-0.06680.17220.04020.00270.4609-0.1809-0.02980.27370.02380.2704-36.753118.92382.0585
130.8224-0.5270.40410.8353-0.88841.03220.07610.2276-0.0576-0.5482-0.07840.06440.35820.24030.04560.4874-0.1709-0.04690.328-0.03210.3405-43.802519.4386-8.8902
140.2977-0.1690.05960.1647-0.02170.00310.1886-0.4446-0.08850.1166-0.0265-0.17020.3349-0.13710.00030.3483-0.1528-0.0330.40250.04160.337-29.627728.99610.6825
150.41690.0427-0.27411.21710.23520.26770.2334-0.12210.2341-0.0053-0.42740.2753-0.1854-0.4058-0.01380.3343-0.32070.00430.3423-0.03410.319-45.210827.88021.1908
160.2985-0.33270.13311.0779-0.25320.07540.0373-0.4536-0.09740.8078-0.25720.33970.4931-0.3906-0.06470.49-0.24650.09930.4237-0.01710.3081-39.937522.92312.9657
170.2112-0.1176-0.12070.20470.16060.13560.141-0.09510.1745-0.2030.03860.166-0.4235-0.31680.00070.4038-0.0965-0.04320.3112-0.01460.3593-42.110833.5485-4.6231
180.26840.11630.07250.04870.04590.0689-0.04380.41480.2669-1.27670.42310.013-0.41080.29190.00760.6425-0.077-0.03720.3699-0.0250.3502-37.98727.3508-21.0284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:26)
2X-RAY DIFFRACTION2(chain A and resid 27:36)
3X-RAY DIFFRACTION3(chain A and resid 37:54)
4X-RAY DIFFRACTION4(chain A and resid 55:85)
5X-RAY DIFFRACTION5(chain A and resid 86:96)
6X-RAY DIFFRACTION6(chain A and resid 97:114)
7X-RAY DIFFRACTION7(chain B and resid 1:15)
8X-RAY DIFFRACTION8(chain B and resid 16:40)
9X-RAY DIFFRACTION9(chain B and resid 41:54)
10X-RAY DIFFRACTION10(chain B and resid 55:94)
11X-RAY DIFFRACTION11(chain B and resid 95:114)
12X-RAY DIFFRACTION12(chain C and resid 1:26)
13X-RAY DIFFRACTION13(chain C and resid 27:40)
14X-RAY DIFFRACTION14(chain C and resid 41:54)
15X-RAY DIFFRACTION15(chain C and resid 55:84)
16X-RAY DIFFRACTION16(chain C and resid 85:93)
17X-RAY DIFFRACTION17(chain C and resid 94:104)
18X-RAY DIFFRACTION18(chain C and resid 105:114)

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