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Basic information

Entry
Database: PDB / ID: 4gro
TitleCrystallographic and biological characterization of N- and C- terminus mutants of human MIF
ComponentsMacrophage migration inhibitory factor
Keywordscytokine / Isomerase / alpha/beta mixture
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 / regulation of macrophage activation / 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 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 / DNA damage response, signal transduction by p53 class mediator / 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 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 / innate immune response / negative regulation of gene expression / 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
Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFan, C. / Lolis, E.
CitationJournal: To be Published
Title: crystallographic and biological characterization of N- and C- terminus mutants of human MIF
Authors: Fan, C. / Lolis, E.
History
DepositionAug 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Derived calculations / Category: struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
D: Macrophage migration inhibitory factor
E: Macrophage migration inhibitory factor
F: Macrophage migration inhibitory factor
G: Macrophage migration inhibitory factor
H: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,90118
Polymers100,5468
Non-polymers35510
Water10,683593
1
A: Macrophage migration inhibitory factor

A: Macrophage migration inhibitory factor

A: Macrophage migration inhibitory factor


Theoretical massNumber of molelcules
Total (without water)37,7053
Polymers37,7053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6700 Å2
ΔGint-39 kcal/mol
Surface area12780 Å2
MethodPISA
2
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
D: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7765
Polymers37,7053
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-61 kcal/mol
Surface area12610 Å2
MethodPISA
3
E: Macrophage migration inhibitory factor
F: Macrophage migration inhibitory factor
H: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9189
Polymers37,7053
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-102 kcal/mol
Surface area12890 Å2
MethodPISA
4
G: Macrophage migration inhibitory factor
hetero molecules

G: Macrophage migration inhibitory factor
hetero molecules

G: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9189
Polymers37,7053
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7500 Å2
ΔGint-102 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.960, 156.960, 96.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-268-

HOH

21A-272-

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: 12568.290 Da / Num. of mol.: 8 / Mutation: Pro1-Ala2 are insertions
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 14, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→15.39 Å / Num. obs: 58450 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 14.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→15.1 Å / SU ML: 0.21 / σ(F): 1.96 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1970 3.45 %
Rwork0.188 --
obs0.189 57105 96 %
all-59642 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0282 Å2-0 Å20 Å2
2---0.0282 Å20 Å2
3---0.0564 Å2
Refinement stepCycle: LAST / Resolution: 2→15.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7044 0 10 593 7647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067204
X-RAY DIFFRACTIONf_angle_d0.9579810
X-RAY DIFFRACTIONf_dihedral_angle_d12.3382598
X-RAY DIFFRACTIONf_chiral_restr0.0681096
X-RAY DIFFRACTIONf_plane_restr0.0041294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0005-2.05040.37911260.30573435X-RAY DIFFRACTION83
2.0504-2.10570.44421190.27033654X-RAY DIFFRACTION91
2.1057-2.16750.38951430.27443999X-RAY DIFFRACTION97
2.1675-2.23720.31171380.25724006X-RAY DIFFRACTION96
2.2372-2.31690.29811340.25943783X-RAY DIFFRACTION95
2.3169-2.40940.33041510.24794008X-RAY DIFFRACTION96
2.4094-2.51850.26711360.25633939X-RAY DIFFRACTION96
2.5185-2.65060.32191480.24153919X-RAY DIFFRACTION96
2.6506-2.81570.35651460.23034005X-RAY DIFFRACTION98
2.8157-3.03150.26941450.20484039X-RAY DIFFRACTION99
3.0315-3.33360.23191280.18044073X-RAY DIFFRACTION99
3.3336-3.80920.15551680.14524087X-RAY DIFFRACTION100
3.8092-4.77390.16041480.12164108X-RAY DIFFRACTION100
4.7739-15.10430.15161400.15174080X-RAY DIFFRACTION99
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)
13.0036-2.39152.55839.6796-6.8277.66730.4401-0.0584-0.16210.1269-0.28610.06220.0970.6599-0.10530.24060.0654-0.01780.2986-0.03450.24189.3129-4.670126.1386
24.9043-1.2409-0.54280.41410.20490.11940.16880.3714-0.1028-0.4305-0.1968-0.30320.56370.6272-0.13670.3860.1230.12330.432-0.0340.230713.24192.43039.9707
32.36840.1010.26032.09920.50381.77130.20070.0338-0.1117-0.08750.0801-0.40010.12750.1733-0.23580.18730.01690.00260.2057-0.06370.195512.0026-0.441221.7634
41.7236-0.07090.48291.5505-0.74352.63230.1661-0.2402-0.02320.3979-0.016-0.6968-0.17610.6039-0.10420.3024-0.0262-0.06850.3036-0.09640.337317.66982.285329.453
51.79080.8624-0.14.2594-0.63641.04580.073-0.10320.02560.23020.0434-0.2558-0.2702-0.0502-0.12870.27560.0072-0.0270.2367-0.04690.149.76574.453927.9741
62.2959-0.7587-1.59256.07931.72822.750.1615-0.4645-0.69480.9353-0.6225-0.08230.570.09570.1790.44110.0131-0.06490.32690.07270.39383.1282-17.961831.2636
71.27870.1218-0.01880.46450.35322.5440.1920.1106-0.215-0.18790.03920.57370.5464-0.3361-0.18010.2593-0.0562-0.04970.2249-0.00610.37228.0447-35.18666.535
82.0852-0.28390.05512.030.71531.98390.21780.0372-0.016-0.1068-0.29460.33570.0907-0.28710.04680.1748-0.013-0.0090.1408-0.03440.234127.242-31.383565.5352
91.6225-0.454-0.20771.80120.11872.71070.10040.07890.11350.1961-0.26070.2773-0.462-0.41670.14710.2530.0459-0.0070.1816-0.04790.302825.2526-23.486966.6315
103.06871.4212-0.24773.15672.20225.56520.3270.8220.1314-0.66830.1004-0.0138-0.6998-0.6321-0.30810.43670.072-0.06290.39320.04010.30736.1216-28.270645.8413
116.4192-4.4521-2.67173.68633.03973.6633-0.00670.03470.51090.4282-0.2682-0.0024-0.0757-0.06370.17270.2717-0.040.02680.2154-0.01130.190239.847-23.635374.2985
120.96290.38411.05660.27961.15095.66540.1744-0.4779-0.20920.86820.10910.28870.2578-0.14010.40330.53630.00180.04890.34790.1410.212147.9607-38.945679.5633
132.13450.2546-0.18571.86540.47112.2630.0581-0.32660.1180.2972-0.18350.19790.04640.27390.0730.2214-0.05560.03360.22260.02710.179144.8553-27.70175.9571
142.51820.2268-0.33911.69030.46871.37490.0766-0.47390.65480.3622-0.1879-0.1839-0.30430.41910.03790.2694-0.11370.0220.3017-0.02580.304650.0532-19.276176.7136
154.5598-1.2409-0.49861.4830.22511.68820.1483-0.25230.3947-0.244-0.124-0.2344-0.02860.2073-0.00560.242-0.04310.02250.14110.02510.229848.0422-23.300969.7492
164.82720.022-2.57021.3083-1.65354.0669-0.136-0.29661.31520.13280.32680.3308-0.382-0.6248-0.19350.37970.03970.04290.3421-0.06890.415325.2535-18.37173.8065
171.3836-0.43110.32840.49170.54441.29080.0492-0.02-0.6406-0.2237-0.1805-0.53650.22580.29740.08760.24120.07420.0440.21830.05030.371245.4938-38.036658.481
182.031-0.27580.13171.5579-0.16562.49270.13010.1652-0.2262-0.1095-0.223-0.07080.00450.40660.12640.17960.0663-0.00820.20620.0240.180445.621-34.631256.3614
191.94390.41060.48571.7607-0.12771.9505-0.00930.5030.0959-0.30680.01980.2392-0.07620.3146-0.04690.24360.0355-0.0280.27510.06430.175443.418-29.178750.6309
205.6952-1.93472.39473.46480.39953.0207-0.52310.06120.43-0.06920.3083-0.6985-0.69760.46140.18250.3249-0.10140.00470.38480.0530.399656.3618-20.188368.6875
211.3610.34520.0642.61380.00840.8753-0.0953-0.515-0.08530.2178-0.0505-0.4891-0.26520.06890.0250.3362-0.0129-0.11440.5014-0.02290.31642.6954-20.274728.1104
222.2247-0.60770.05051.0879-0.03220.7789-0.1581-1.0772-0.34560.34430.0551-0.1488-0.22590.03050.0260.24940.0835-0.09080.43160.11130.201238.9608-21.982427.6783
231.8346-0.5526-0.09552.80210.69971.6782-0.2833-0.732-0.2170.08050.09780.3129-0.2779-0.19860.13850.2490.0778-0.01720.47080.0420.257730.9722-21.974427.1025
242.1232-2.22241.13492.403-0.87152.9379-0.2632-0.2917-0.8745-0.10370.0677-0.36720.7906-0.04580.14640.2028-0.01770.06530.39720.12950.504742.6034-41.248917.4907
252.4945-0.3075-0.30050.31350.06651.5103-0.2102-0.35320.5882-0.14310.1086-0.1899-0.81360.0640.05020.4822-0.1073-0.01850.2092-0.05570.411843.0072-9.553612.1346
260.74540.24430.42070.74410.4031.8098-0.3392-0.13140.6568-0.4137-0.0024-0.1707-1.1771-0.0669-0.13440.51160.0662-0.06160.0608-0.11920.34539.6613-10.764910.0307
271.88770.2566-0.18321.61990.11342.4112-0.30640.13880.0463-0.61570.0385-0.0743-0.7175-0.26470.18180.5224-0.0033-0.04590.2117-0.03420.245935.7061-13.59593.7023
281.7192-1.0578-2.162.89861.24792.9109-0.3015-0.66060.05390.0262-0.0090.7129-0.5679-0.37220.22690.33160.0818-0.110.4713-0.06270.275824.8029-16.108325.4953
291.10660.32360.0822.4729-0.36831.95520.13960.2706-0.2668-0.58680.1402-0.21070.36990.3471-0.26610.39290.05580.05630.4535-0.12450.28959.778-5.263870.573
301.20930.55640.43181.21530.69231.77710.23050.4264-0.3932-0.22430.2678-0.62930.53170.603-0.09160.34110.1032-0.02310.2412-0.16370.341610.7914-5.392174.5468
311.44260.25350.08961.97490.26871.78350.34170.0608-0.21240.09740.1555-0.52620.03810.4879-0.26030.23750.0334-0.02420.3161-0.14420.346714.3403-2.828781.2723
322.38870.8988-0.72414.26610.82680.54290.08080.1153-0.80830.19840.22190.17380.56060.1328-0.24420.39750.0051-0.18140.33140.00210.3618-4.8956-17.719384.085
333.2739-0.8426-2.05282.70932.52332.9277-0.11620.24490.25250.1204-0.15470.12070.057-0.34420.09880.18880.0407-0.02760.22750.03440.30345.421-26.8098.338
340.1282-0.19130.19570.5015-0.44580.41070.14340.24770.365-0.1597-0.07140.0807-0.4401-0.28560.22620.39820.3788-0.05010.19270.02530.969759.962-25.88616.83
351.9944-0.8730.54630.66620.2460.94230.14111.08640.9717-0.3710.02970.0958-0.42810.23320.87710.36220.0355-0.08890.51730.37860.516953.091-32.1763.479
362.39460.06350.66221.03340.43780.9527-0.16640.38640.56680.05220.1087-0.0944-0.3892-0.21290.07310.26330.0287-0.04980.21130.05960.292346.9-28.54312.76
372.4806-0.8598-0.22772.07880.73072.3888-0.27470.53131.17350.22260.2946-0.5223-0.34320.13820.02540.2897-0.0642-0.13580.34220.160.591849.087-38.70710.717
381.88540.41680.66490.8304-0.17822.4756-0.10160.36220.56650.444-0.1262-0.26580.0645-0.0764-0.0030.21810.0459-0.06610.25820.04170.367942.638-32.51413.729
391.56950.17922.00982.1145-0.22172.7949-0.2730.74510.3558-0.47950.00220.09750.2283-0.15850.03290.2248-0.07270.04380.54560.0430.30737.149-18.128-3.734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 90 )
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 108 )
6X-RAY DIFFRACTION6chain 'A' and (resid 109 through 117 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 20 )
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 66 )
9X-RAY DIFFRACTION9chain 'B' and (resid 67 through 108 )
10X-RAY DIFFRACTION10chain 'B' and (resid 109 through 117 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 10 )
12X-RAY DIFFRACTION12chain 'C' and (resid 11 through 20 )
13X-RAY DIFFRACTION13chain 'C' and (resid 21 through 66 )
14X-RAY DIFFRACTION14chain 'C' and (resid 67 through 90 )
15X-RAY DIFFRACTION15chain 'C' and (resid 91 through 108 )
16X-RAY DIFFRACTION16chain 'C' and (resid 109 through 117 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 20 )
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 66 )
19X-RAY DIFFRACTION19chain 'D' and (resid 67 through 108 )
20X-RAY DIFFRACTION20chain 'D' and (resid 109 through 117 )
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 20 )
22X-RAY DIFFRACTION22chain 'E' and (resid 21 through 66 )
23X-RAY DIFFRACTION23chain 'E' and (resid 67 through 108 )
24X-RAY DIFFRACTION24chain 'E' and (resid 109 through 117 )
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 20 )
26X-RAY DIFFRACTION26chain 'F' and (resid 21 through 66 )
27X-RAY DIFFRACTION27chain 'F' and (resid 67 through 108 )
28X-RAY DIFFRACTION28chain 'F' and (resid 109 through 117 )
29X-RAY DIFFRACTION29chain 'G' and (resid 1 through 20 )
30X-RAY DIFFRACTION30chain 'G' and (resid 21 through 66 )
31X-RAY DIFFRACTION31chain 'G' and (resid 67 through 108 )
32X-RAY DIFFRACTION32chain 'G' and (resid 109 through 117 )
33X-RAY DIFFRACTION33chain 'H' and (resid 1 through 10 )
34X-RAY DIFFRACTION34chain 'H' and (resid 11 through 20 )
35X-RAY DIFFRACTION35chain 'H' and (resid 21 through 33 )
36X-RAY DIFFRACTION36chain 'H' and (resid 34 through 71 )
37X-RAY DIFFRACTION37chain 'H' and (resid 72 through 90 )
38X-RAY DIFFRACTION38chain 'H' and (resid 91 through 108 )
39X-RAY DIFFRACTION39chain 'H' and (resid 109 through 117 )

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