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- PDB-2gdg: Crystal structure of covalently modified macrophage inhibitory factor -

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Basic information

Entry
Database: PDB / ID: 2gdg
TitleCrystal structure of covalently modified macrophage inhibitory factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / Pro-1 pucker
Function / homology
Function and homology information


Cell surface interactions at the vascular wall / 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 / positive regulation of adaptive immune response / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway ...Cell surface interactions at the vascular wall / 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 / positive regulation of adaptive immune response / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway / 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 / negative regulation of protein metabolic process / prostaglandin biosynthetic process / carboxylic acid metabolic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / protein homotrimerization / positive regulation of protein kinase A signaling / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of cellular senescence / DNA damage response, signal transduction by p53 class mediator / positive regulation of B cell proliferation / positive regulation of phosphorylation / Neutrophil degranulation / negative regulation of cell migration / cytokine activity / positive regulation of cytokine production / positive regulation of MAP kinase activity / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of tumor necrosis factor production / myelin sheath / positive regulation of peptidyl-serine phosphorylation / 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 / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / cell surface / extracellular space / 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
Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGolubkov, P.A. / Hackert, M.L.
CitationJournal: Bioorg.Chem. / Year: 2006
Title: Inactivation of the phenylpyruvate tautomerase activity of macrophage migration inhibitory factor by 2-oxo-4-phenyl-3-butynoate.
Authors: Golubkov, P.A. / Johnson Jr., W.H. / Czerwinski, R.M. / Person, M.D. / Wang, S.C. / Whitman, C.P. / Hackert, M.L.
History
DepositionMar 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor


Theoretical massNumber of molelcules
Total (without water)37,1493
Polymers37,1493
Non-polymers00
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-37 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.705, 94.705, 87.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a trimer of the asymmetric unit.

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Components

#1: Protein Macrophage migration inhibitory factor / / MIF / Phenylpyruvate tautomerase / Glycosylation-inhibiting factor / GIF / Delayed early response ...MIF / Phenylpyruvate tautomerase / Glycosylation-inhibiting factor / GIF / Delayed early response protein 6 / DER6


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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS / References: UniProt: P34884, phenylpyruvate tautomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 8000, 0.05M sodium phosphate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 23, 2002
RadiationMonochromator: bent cylindrical Si-mirror (Rh coating); Si(111) double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 78970 / Num. obs: 76879 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3
Reflection shellResolution: 1.45→1.5 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MFF

1mff


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.017 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Ambiguous inhibitor density; inhibitor coordinates not included.
RfactorNum. reflection% reflectionSelection details
Rfree0.18304 3872 5 %RANDOM
Rwork0.14665 ---
all0.1485 73005 --
obs0.1485 73005 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 0 465 3072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.05
X-RAY DIFFRACTIONbond angles (degrees)3.57
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 278 -
Rwork0.217 5323 -
obs--96.77 %

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