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- PDB-1mfi: CRYSTAL STRUCTURE OF MACROPHAGE MIGRATION INHIBITORY FACTOR COMPL... -

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Basic information

Entry
Database: PDB / ID: 1mfi
TitleCRYSTAL STRUCTURE OF MACROPHAGE MIGRATION INHIBITORY FACTOR COMPLEXED WITH (E)-2-FLUORO-P-HYDROXYCINNAMATE
ComponentsPROTEIN (MACROPHAGE MIGRATION INHIBITORY FACTOR)
KeywordsVIRAL PROTEIN / CYTOKINE / MACROPHAGE / INFLAMMATORY RESPONSE / TAUTOMERASE
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 / Cell surface interactions at the vascular wall / phenylpyruvate tautomerase / L-dopachrome isomerase / positive regulation of adaptive immune response / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / Cell surface interactions at the vascular wall / phenylpyruvate tautomerase / L-dopachrome isomerase / positive regulation of adaptive immune response / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / 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 / 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 B cell proliferation / Neutrophil degranulation / cytokine activity / positive regulation of MAP kinase activity / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / myelin sheath / regulation of cell population proliferation / protease binding / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / positive regulation of protein phosphorylation / negative regulation of gene expression / innate immune response / protein-containing complex binding / negative regulation of apoptotic process / cell surface / extracellular space / nucleoplasm / identical protein binding / plasma membrane / 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
2-FLUORO-3-(4-HYDROXYPHENYL)-2E-PROPENEOATE / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTaylor, A.B. / Johnson Jr., W.H. / Czerwinski, R.M. / Whitman, C.P. / Hackert, M.L.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of macrophage migration inhibitory factor complexed with (E)-2-fluoro-p-hydroxycinnamate at 1.8 A resolution: implications for enzymatic catalysis and inhibition.
Authors: Taylor, A.B. / Johnson Jr., W.H. / Czerwinski, R.M. / Li, H.S. / Hackert, M.L. / Whitman, C.P.
History
DepositionAug 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MACROPHAGE MIGRATION INHIBITORY FACTOR)
B: PROTEIN (MACROPHAGE MIGRATION INHIBITORY FACTOR)
C: PROTEIN (MACROPHAGE MIGRATION INHIBITORY FACTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6926
Polymers37,1493
Non-polymers5433
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-32 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.530, 99.530, 105.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.37931, 0.2986, 0.87576), (-0.87343, 0.19682, -0.44541), (-0.30537, -0.93386, 0.18614)-12.13242, 19.18984, 24.3611
2given(-0.38447, -0.87668, -0.28917), (0.2845, 0.18548, -0.94056), (0.87821, -0.44388, 0.1781)19.6363, 23.06759, 14.58429

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Components

#1: Protein PROTEIN (MACROPHAGE MIGRATION INHIBITORY FACTOR) / PHENYLPYRUVATE TAUTOMERASE


Mass: 12383.024 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MIF / Plasmid: PET11B / Gene (production host): MUMIF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P34884
#2: Chemical ChemComp-FHC / 2-FLUORO-3-(4-HYDROXYPHENYL)-2E-PROPENEOATE / (E)-2-FLUORO-P-HYDROXYCINNAMATE


Mass: 181.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H6FO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.7 Å3/Da / Density % sol: 54 %
Description: THE STARTING MODEL WAS SOLVED WITH PDB ENTRY 1MIF
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
116 mg/mlprotein1drop
220 mMTris1droppH7.4
320 mM1dropNaCl
430 %PEG80001reservoir
550 mMsodium phosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: MSC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35875 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.076 / Net I/σ(I): 5.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.33 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Num. measured all: 207686 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / % possible obs: 97.1 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.6 ANGSTROMS RESOLUTION NATIVE STRUCTURE OF MACROPHAGE MIGRATION INHIBITORY FACTOR FROM MOUSE

Resolution: 1.8→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED, REFMAC USED
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1792 5 %RANDOM
Rwork0.178 ---
obs0.178 35875 99.1 %-
Displacement parametersBiso mean: 33.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-50 Å
Luzzati sigma a0.18 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 39 93 2739
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.96
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.913
X-RAY DIFFRACTIONx_mcangle_it2.975
X-RAY DIFFRACTIONx_scbond_it5.647
X-RAY DIFFRACTIONx_scangle_it8.969
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 168 4.8 %
Rwork0.336 3349 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
X-RAY DIFFRACTION3FHC.PARFHC.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.96

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