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- PDB-4plu: Crystal structure of Macrophage Migration Inhibitory Factor in co... -

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Basic information

Entry
Database: PDB / ID: 4plu
TitleCrystal structure of Macrophage Migration Inhibitory Factor in complex with benzaldehyde
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / Covalent inhibitor / Isomerase / active site / ISOMERASE-ISOMERASE INHIBITOR complex
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
benzaldehyde / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsPantouris, G. / Lolis, E.
CitationJournal: Chem.Biol. / Year: 2015
Title: An Analysis of MIF Structural Features that Control Functional Activation of CD74.
Authors: Pantouris, G. / Syed, M.A. / Fan, C. / Rajasekaran, D. / Cho, T.Y. / Rosenberg, E.M. / Bucala, R. / Bhandari, V. / Lolis, E.J.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)37,69610
Polymers37,0653
Non-polymers6317
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-37 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.601, 67.812, 88.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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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 / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-HBX / benzaldehyde


Mass: 106.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STARTING COMPOUND IS S-(3,4-DIHYDROISOQUINOLIN-1-YL) BENZOTHIOATE. PRO-1 ATTACKS THE C=O GROUP ...THE STARTING COMPOUND IS S-(3,4-DIHYDROISOQUINOLIN-1-YL) BENZOTHIOATE. PRO-1 ATTACKS THE C=O GROUP OF THE COMPOUND FORMING A COVALENT BOND AND RELEASING THE REST OF THE COMPOUND. BENZALDEHYDE (HBX) IS THE REMAINING GROUP THAT FORMS COVALENT BOND WITH THE PROTEIN.

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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: 54.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium Sulphate, 3% 2-propanol,20 mM Tris.HCl pH 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 50847 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.029 / Χ2: 0.951 / Net I/av σ(I): 36.836 / Net I/σ(I): 26.5 / Num. measured all: 237341
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.63-1.664.50.21424811.08597.6
1.66-1.694.60.1825171.21798.3
1.69-1.724.60.16324881.27299
1.72-1.764.60.13924901.30398.7
1.76-1.794.60.12125301.5198.7
1.79-1.844.60.09925241.52898.9
1.84-1.884.60.0825361.27399.1
1.88-1.934.70.06824951.21599.2
1.93-1.994.70.05625551.04599.5
1.99-2.054.70.04825330.93599.5
2.05-2.134.70.04225400.80999.5
2.13-2.214.70.03825440.77499.5
2.21-2.314.70.03525430.74399.1
2.31-2.434.70.03325500.70999.5
2.43-2.594.80.03125820.68399.7
2.59-2.794.80.02825800.63799.7
2.79-3.074.80.02725850.66999.8
3.07-3.514.80.02625760.61798.2
3.51-4.424.70.02425420.57596.1
4.42-504.50.02326560.54895

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→42.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 2581 5.1 %RANDOM
Rwork0.1825 48206 --
obs0.1842 50787 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.43 Å2 / Biso mean: 15.132 Å2 / Biso min: 5.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.63→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 46 354 2922
Biso mean--26.99 28.65 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192627
X-RAY DIFFRACTIONr_bond_other_d00.022443
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.9723571
X-RAY DIFFRACTIONr_angle_other_deg4.713.0045597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61424.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.41815382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.054159
X-RAY DIFFRACTIONr_chiral_restr0.1240.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213023
X-RAY DIFFRACTIONr_gen_planes_other0.0260.02606
X-RAY DIFFRACTIONr_mcbond_it1.5381.3031363
X-RAY DIFFRACTIONr_mcbond_other1.5381.3031362
X-RAY DIFFRACTIONr_mcangle_it2.0881.9561697
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A60080.11
12B60080.11
21A58900.1
22C58900.1
31B59690.09
32C59690.09
LS refinement shellResolution: 1.629→1.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 182 -
Rwork0.234 3479 -
all-3661 -
obs--97.76 %

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