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- PDB-2ooh: Crystal Structure of MIF bound to a Novel Inhibitor, OXIM-11 -

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Basic information

Entry
Database: PDB / ID: 2ooh
TitleCrystal Structure of MIF bound to a Novel Inhibitor, OXIM-11
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / alternative ligand-binding modes
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 / 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
4-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCrichlow, G.V. / Al-Abed, Y. / Lolis, E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Alternative chemical modifications reverse the binding orientation of a pharmacophore scaffold in the active site of macrophage migration inhibitory factor.
Authors: Crichlow, G.V. / Cheng, K.F. / Dabideen, D. / Ochani, M. / Aljabari, B. / Pavlov, V.A. / Miller, E.J. / Lolis, E. / Al-Abed, Y.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,51215
Polymers37,0653
Non-polymers1,44712
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-136 kcal/mol
Surface area12820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.595, 95.595, 103.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains one homotrimer of MIF, which is presumed to be thre biological unit.

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Components

#1: Protein Macrophage migration inhibitory factor / MIF / Phenylpyruvate tautomerase / Glycosylation-inhibiting factor / GIF / (EC 5.3.2.1)


Mass: 12355.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIF / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14174, phenylpyruvate tautomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OX3 / 4-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME


Mass: 247.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.67 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50% saturated ammonium sulfate, 4% isopropanol, 0.1 M tris(hydroxymethyl)aminomethane,mixed with protein:inhibitor complex in a 1:1 ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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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: 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: 1.85→110 Å / Num. obs: 46128 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.334 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.9240.3544511.302196
1.92-1.9940.24144311.168195.1
1.99-2.084.10.18445041.178197.4
2.08-2.194.20.14245691.116198.2
2.19-2.334.30.11645901.181198.8
2.33-2.514.50.09946891.178199.7
2.51-2.764.70.08346431.334199.8
2.76-3.165.10.06546951.383199.6
3.16-3.995.60.04747241.613199.2
3.99-1105.60.03748321.597198

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Phasing

Phasing MRRfactor: 0.332 / Cor.coef. Fo:Fc: 0.727 / Cor.coef. Io to Ic: 0.67
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LJT

1ljt


Resolution: 1.85→110 Å / Isotropic thermal model: isotropic
Cross valid method: throughout, until most of the model was completed, then all observed data were used in some of the later refinement rounds. (R-free value quoted is that obtained before refinement ...Cross valid method: throughout, until most of the model was completed, then all observed data were used in some of the later refinement rounds. (R-free value quoted is that obtained before refinement was performed against all data).
σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: OXIM-11 molecules were modelled with partial occupancies. Glycerol molecules modelled in the same active sites as OXIM-11 have occupancies were modlled as having occupancies equal to 1-(OXIM- ...Details: OXIM-11 molecules were modelled with partial occupancies. Glycerol molecules modelled in the same active sites as OXIM-11 have occupancies were modlled as having occupancies equal to 1-(OXIM-11 occupancy for that active site). The ratio of OXIM-11 to glycerol occupancy for each active site was determined by occupancy refinement in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2228 -random
Rwork0.191 ---
obs0.192 44612 95.1 %-
all-46116 --
Displacement parametersBiso mean: 22.76 Å2
Refinement stepCycle: LAST / Resolution: 1.85→110 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 88 305 2979

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