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- PDB-4gum: Cystal structure of locked-trimer of human MIF -

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Basic information

Entry
Database: PDB / ID: 4gum
TitleCystal structure of locked-trimer of human MIF
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / alpha/beta mixture / cytokine and 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 / carboxylic acid metabolic 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 / carboxylic acid metabolic process / negative regulation of mature B cell apoptotic process / negative regulation of macrophage chemotaxis / 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 / negative regulation of DNA damage response, signal transduction by p53 class mediator / chemoattractant activity / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytokine activity / negative regulation of cell migration / positive regulation of fibroblast proliferation / Cell surface interactions at the vascular wall / positive regulation of cytokine production / positive regulation of tumor necrosis factor production / protease binding / secretory granule lumen / ficolin-1-rich granule lumen / vesicle / positive regulation of ERK1 and ERK2 cascade / innate immune response / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / 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
Macrophage migration inhibitory factor / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsFan, C. / Lolis, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: MIF intersubunit disulfide mutant antagonist supports activation of CD74 by endogenous MIF trimer at physiologic concentrations.
Authors: Fan, C. / Rajasekaran, D. / Syed, M.A. / Leng, L. / Loria, J.P. / Bhandari, V. / Bucala, R. / Lolis, E.J.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 18, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _entity.pdbx_ec / _entity_name_com.name ..._entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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
I: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,38017
Polymers111,0979
Non-polymers2848
Water2,324129
1
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1396
Polymers37,0323
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-72 kcal/mol
Surface area15380 Å2
MethodPISA
2
D: Macrophage migration inhibitory factor
E: Macrophage migration inhibitory factor
F: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1747
Polymers37,0323
Non-polymers1424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-80 kcal/mol
Surface area15020 Å2
MethodPISA
3
G: Macrophage migration inhibitory factor
H: Macrophage migration inhibitory factor
I: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0684
Polymers37,0323
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-50 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.315, 100.381, 199.480
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: 12344.096 Da / Num. of mol.: 9 / Mutation: N110C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Plasmid: pET11b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14174, UniProt: Q6DN04*PLUS, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 45.75 %
Crystal growTemperature: 293 K / pH: 8
Details: 0.2M LiSO4, 3% DMSO, pH8.0, 33% PEG4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 43492 / % possible obs: 98.7 % / Observed criterion σ(I): 4.95 / Redundancy: 10.9 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 22.94
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 4.95 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→48.79 Å / SU ML: 0.4 / Isotropic thermal model: isotropic / σ(F): 1.37 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 2184 5.03 %
Rwork0.222 --
obs0.225 43425 98.5 %
all-44065 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.38 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1903 Å20 Å20 Å2
2--0.1895 Å2-0 Å2
3----0.3798 Å2
Refinement stepCycle: LAST / Resolution: 2.33→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7387 0 8 129 7524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037571
X-RAY DIFFRACTIONf_angle_d0.64810282
X-RAY DIFFRACTIONf_dihedral_angle_d12.6142694
X-RAY DIFFRACTIONf_chiral_restr0.0481159
X-RAY DIFFRACTIONf_plane_restr0.0031340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3322-2.38290.36941280.29682463X-RAY DIFFRACTION95
2.3829-2.43830.3351420.28732531X-RAY DIFFRACTION99
2.4383-2.49930.30561470.26462535X-RAY DIFFRACTION98
2.4993-2.56690.30021190.25022533X-RAY DIFFRACTION98
2.5669-2.64240.36311430.27542520X-RAY DIFFRACTION98
2.6424-2.72770.29581450.2412521X-RAY DIFFRACTION98
2.7277-2.82520.28141360.24172543X-RAY DIFFRACTION98
2.8252-2.93830.32721180.23932559X-RAY DIFFRACTION98
2.9383-3.0720.30531260.26352545X-RAY DIFFRACTION99
3.072-3.23390.31491330.24152568X-RAY DIFFRACTION98
3.2339-3.43650.28351390.22132567X-RAY DIFFRACTION99
3.4365-3.70170.26071620.21682574X-RAY DIFFRACTION99
3.7017-4.07410.26621320.20062614X-RAY DIFFRACTION99
4.0741-4.66320.24121340.18672648X-RAY DIFFRACTION99
4.6632-5.87360.23091190.20762707X-RAY DIFFRACTION100
5.8736-48.79770.2581610.22152813X-RAY DIFFRACTION100
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)
11.1271-0.0858-0.79182.0560.71251.4855-0.0048-0.0478-0.1955-0.1093-0.1749-0.04380.26730.1191-0.01270.2286-0.06680.01460.2588-0.00150.351-12.933-22.3926-29.6914
20.9536-0.2375-0.12980.43090.58853.785-0.0994-0.1956-0.34830.1165-0.03580.11690.3335-1.1788-0.00880.3973-0.09150.05050.52490.03670.3898-28.5966-23.7584-14.3941
33.28460.1402-0.4361.7462-0.48293.8713-0.1465-0.14470.29360.52240.07290.1518-0.2731-0.1171-0.00880.2961-0.0325-0.00730.3101-0.02570.2984-14.3861-7.7871-13.2237
42.60860.50351.07341.14920.74322.4640.1726-0.1093-0.28150.2118-0.2004-0.08210.1406-0.1950.05430.2557-0.0014-0.0230.2440.04870.3612-12.1822.195-55.1264
50.5005-0.08440.17680.96970.41482.6770.05210.03670.18970.25070.1162-0.12630.05630.57120.00020.4261-0.011-0.01260.35470.00550.37713.15823.4515-40.0036
61.8807-0.72730.17271.8148-2.19634.334-0.24610.1354-0.31490.13710.14680.23490.3036-0.4881-0.04130.4259-0.0350.08950.33860.02050.3879-11.28077.1539-38.701
71.25460.2991-0.8080.94280.65171.27170.0314-0.59410.05830.59210.3494-0.07960.6731.70810.85320.41390.1764-0.14581.1878-0.3740.47230.824416.350221.8452
80.77240.11510.06161.73110.87713.5111-0.19360.1564-0.63880.84480.5704-0.0682.80721.40240.2690.98240.3281-0.12780.1579-0.08150.3293-16.23172.062716.7003
92.6067-0.303-0.95491.87070.46214.35190.2041-0.11530.03870.1574-0.0447-0.1002-0.15920.12260.04060.129-0.0042-0.06920.3046-0.03140.2581-14.237121.07466.4725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:114 )
2X-RAY DIFFRACTION2(CHAIN B AND RESID 1:114 )
3X-RAY DIFFRACTION3(CHAIN C AND RESID 1:114 )
4X-RAY DIFFRACTION4(CHAIN D AND RESID 1:114 )
5X-RAY DIFFRACTION5(CHAIN E AND RESID 1:114 )
6X-RAY DIFFRACTION6(CHAIN F AND RESID 1:113 )
7X-RAY DIFFRACTION7(CHAIN G AND RESID 1:114 )
8X-RAY DIFFRACTION8(CHAIN H AND RESID 1:111 )
9X-RAY DIFFRACTION9(CHAIN I AND RESID 1:113 )

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