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- PDB-3ce4: Structure of Macrophage Migration Inhibitory Factor Covalently In... -

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Basic information

Entry
Database: PDB / ID: 3ce4
TitleStructure of Macrophage Migration Inhibitory Factor Covalently Inhibited by PMSF Treatment
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / covalent modification / covalent inhibition / Cytokine / Inflammatory response / Phosphoprotein
Function / homology
Function and homology information


: / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / 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 myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / 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
ISOPROPYL ALCOHOL / PHENYLMETHYLSULFONYL FLUORIDE / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsCrichlow, G.V. / Lolis, E.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and kinetic analyses of macrophage migration inhibitory factor active site interactions.
Authors: Crichlow, G.V. / Lubetsky, J.B. / Leng, L. / Bucala, R. / Lolis, E.J.
History
DepositionFeb 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Apr 23, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_modification_feature.auth_comp_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.ref_comp_id / _pdbx_modification_feature.ref_pcm_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_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)38,46516
Polymers37,0653
Non-polymers1,39913
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-76.4 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.403, 67.505, 88.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: MIF, GLIF, MMIF / Plasmid: pET11b / 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 , 5 types, 477 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PMF / phenylmethylsulfonyl fluoride / PMSF


Mass: 174.193 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H7FO2S / Comment: protease inhibitor*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 50% saturated ammonium sulfate, 4% isopropanol, 0.1M tris(hydroxymethyl)aminomethane; mixed with protein:inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 17, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. obs: 58940 / % possible obs: 99.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 21
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.316 / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.343 / Cor.coef. Fo:Fc: 0.713 / Cor.coef. Io to Ic: 0.654
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA7

1ca7


Resolution: 1.55→53.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.83 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1202 2 %RANDOM
Rwork0.195 ---
obs0.195 57737 99.1 %-
all-57737 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.076 Å0.071 Å
Refinement stepCycle: LAST / Resolution: 1.55→53.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 81 464 3119
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 85 -
Rwork0.436 3882 -
obs--91.47 %
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)
11.86050.00770.27361.28870.93961.12680.04880.1719-0.0348-0.12760.0341-0.0889-0.01980.1095-0.0829-0.0064-0.0062-0.007-0.04220.00440.099632.67410.479-1.809
22.52331.05461.02191.92240.35440.53660.0612-0.03880.0376-0.0833-0.0572-0.0324-0.0177-0.0034-0.00410.001-0.00780.0045-0.0334-0.00680.092129.39712.3361.942
30.4712-0.05920.49290.8317-0.00211.4382-0.00260.02750.0283-0.0222-0.00610.0478-0.12990.00910.0087-0.025-0.0102-0.0136-0.0547-0.00320.111324.78716.0255.974
43.9005-1.93251.06822.3433-0.80281.56370.2070.262-0.2536-0.285-0.0540.15410.26420.0381-0.1530.0345-0.0027-0.0662-0.0532-0.00160.113318.923-7.2751.576
50.8529-0.3670.47840.9103-0.44511.1840.07920.0407-0.1218-0.12250.00630.27290.1004-0.0542-0.08550.011-0.0084-0.0725-0.06070.00660.176216.154-3.2464.347
60.6346-0.38350.26881.9877-0.54340.65510.0524-0.0521-0.1261-0.01660.04850.38820.0845-0.1003-0.1009-0.0364-0.006-0.0318-0.0570.01180.163312.7520.89.231
71.11250.1721-1.17441.6696-0.51572.16-0.0068-0.0302-0.05590.0584-0.0161-0.10170.15260.08180.0229-0.0004-0.0061-0.0347-0.05710.01040.12335.786-4.04815.609
80.37560.4241-0.4732.3315-0.85451.29170.0341-0.0562-0.03520.1712-0.0361-0.01760.04610.06790.002-0.00910.0023-0.0177-0.02660.01360.123931.994-0.52517.518
91.05890.00060.07991.01190.00210.61690.0532-0.1385-0.06590.2089-0.01990.02370.0261-0.0072-0.03340.0074-0.01130.0029-0.05660.01590.104428.0794.0421.218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 54
3X-RAY DIFFRACTION3A55 - 114
4X-RAY DIFFRACTION4B1 - 21
5X-RAY DIFFRACTION5B22 - 54
6X-RAY DIFFRACTION6B55 - 114
7X-RAY DIFFRACTION7C1 - 23
8X-RAY DIFFRACTION8C24 - 54
9X-RAY DIFFRACTION9C55 - 114

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