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- PDB-4pkk: Crystal structure of Macrophage Migration inhibitory factor in co... -

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Basic information

Entry
Database: PDB / ID: 4pkk
TitleCrystal structure of Macrophage Migration inhibitory factor in complex with furan-2-ylmethyl)imino methanethiol
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / Inhibitor / Complex / 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 lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / negative regulation of myeloid cell apoptotic process ...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 lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate secretion / 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 chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / prostaglandin biosynthetic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / 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 cytokine production / cytokine activity / Cell surface interactions at the vascular wall / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / 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 / 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
(Z)-[(furan-2-ylmethyl)imino]methanethiol / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsPantouris, G. / Lolis, E.
CitationJournal: To Be Published
Title: Crystal structure of Macrophage Migration inhibitory factor with a covalent inhibitor
Authors: Pantouris, G. / Lolis, E.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: 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
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)38,38617
Polymers37,0653
Non-polymers1,32114
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-71 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.702, 95.702, 103.662
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
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 / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1 - 1121 - 112
21THRTHRBB1 - 1121 - 112
12THRTHRAA1 - 1121 - 112
22THRTHRCC1 - 1121 - 112
13ALAALABB1 - 1141 - 114
23ALAALACC1 - 1141 - 114

NCS ensembles :
ID
1
2
3

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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 / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase

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Non-polymers , 5 types, 386 molecules

#2: Chemical ChemComp-31E / (Z)-[(furan-2-ylmethyl)imino]methanethiol


Mass: 141.191 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H7NOS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.7 Å3/Da / Density % sol: 66.73 %
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: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 52989 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.027 / Χ2: 0.821 / Net I/av σ(I): 66.085 / Net I/σ(I): 23.7 / Num. measured all: 421819
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.78-1.817.70.12926250.833100
1.81-1.847.80.11726020.874100
1.84-1.887.80.10226340.966100
1.88-1.927.80.08926151.079100
1.92-1.967.80.08126311.142100
1.96-27.90.07325701.158100
2-2.057.90.06526711.202100
2.05-2.117.90.05626111.094100
2.11-2.1780.04926590.988100
2.17-2.2480.04326150.883100
2.24-2.3280.03626240.769100
2.32-2.4280.03326420.696100
2.42-2.538.10.0326270.637100
2.53-2.668.10.02726760.629100
2.66-2.838.10.02426380.623100
2.83-3.048.10.02126570.595100
3.04-3.358.10.01826650.568100
3.35-3.838.10.01727030.566100
3.83-4.838.10.01727060.55899.9
4.83-507.80.01628180.6599.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.78→47.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 2693 5.1 %RANDOM
Rwork0.1616 50260 --
obs0.1626 52953 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.82 Å2 / Biso mean: 17.949 Å2 / Biso min: 10.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.78→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 82 372 2985
Biso mean--23.86 30.72 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022662
X-RAY DIFFRACTIONr_bond_other_d00.022495
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9773613
X-RAY DIFFRACTIONr_angle_other_deg3.6973.0095711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.54224.54599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.77615383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.914159
X-RAY DIFFRACTIONr_chiral_restr0.1270.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213032
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02603
X-RAY DIFFRACTIONr_mcbond_it1.5231.5781361
X-RAY DIFFRACTIONr_mcbond_other1.5111.5771360
X-RAY DIFFRACTIONr_mcangle_it1.9742.3611696
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A57190.14
12B57190.14
21A56900.13
22C56900.13
31B59650.13
32C59650.13
LS refinement shellResolution: 1.78→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 207 -
Rwork0.19 3655 -
all-3862 -
obs--99.95 %

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