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- PDB-2oow: MIF Bound to a Fluorinated OXIM Derivative -

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Basic information

Entry
Database: PDB / ID: 2oow
TitleMIF Bound to a Fluorinated OXIM Derivative
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 / phenylpyruvate tautomerase / L-dopachrome isomerase / 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 ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / 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 / carboxylic acid metabolic process / 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 / 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 tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / 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 / 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
ISOPROPYL ALCOHOL / Chem-OX4 / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 26, 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: Non-polymer description / Version format compliance
Revision 1.3Jun 13, 2012Group: Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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)38,80919
Polymers37,0653
Non-polymers1,74416
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.610, 67.794, 87.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9999, -0.0112, 0.0031), (0.0108, -0.7932, 0.6089), (-0.0044, 0.6089, 0.7932)174.4428, -1.514, 0.7045
DetailsThe asymmetric unit contains one homotrimer of MIF, which is presumed to be the physiologically active entity

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Components

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Protein , 1 types, 3 molecules ABC

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


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

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Non-polymers , 5 types, 276 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OX4 / 3-FLUORO-4-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME


Mass: 265.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16FNO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 54.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50% saturated ammonium sulfate, 4% isopropanol, 0.1 M tris(hydroxymethyl)aminomethan; 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

Diffraction
IDMean temperature (K)Crystal-ID
1931
21
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
2
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 16, 2006 / Details: mirrors
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→100 Å / Num. obs: 41057 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.287 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.814.50.44140220.9781,2100
1.81-1.894.60.28840401.0391,2100
1.89-1.974.60.240621.1811,2100
1.97-2.074.70.13940551.0511,2100
2.07-2.24.70.10740591.1061,2100
2.2-2.384.70.08740741.191,2100
2.38-2.614.80.07240971.2841,2100
2.61-2.994.80.05741321.3351,2100
2.99-3.774.80.04741651.5731,2100
3.77-1004.60.04343512.0541,299.8

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Phasing

Phasing MRRfactor: 0.333 / Cor.coef. Fo:Fc: 0.735 / Cor.coef. Io to Ic: 0.686
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 2OOH

2ooh


Resolution: 1.75→100 Å / FOM work R set: 0.881 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STATISTICS LISTED BY RESOLUTION SHELL ARE FROM THE LAST ROUND OF CNS REFINEMENT. MINOR MANUAL ADJUSTEMENTS WERE PERFORMED AFTERWARDS. THE OVERALL STATISTICS REPRESENT THE FINAL MODEL. ...Details: THE STATISTICS LISTED BY RESOLUTION SHELL ARE FROM THE LAST ROUND OF CNS REFINEMENT. MINOR MANUAL ADJUSTEMENTS WERE PERFORMED AFTERWARDS. THE OVERALL STATISTICS REPRESENT THE FINAL MODEL. INHIBITOR MOLECULES WERE MODELLED WITH PARTIAL OCCUPANCIES. GLYCEROL MOLECULES MODELLED IN THE SAME ACTIVE SITES AS INHIBITOR HAVE OCCUPANCIES WERE MODLLED AS HAVING OCCUPANCIES EQUAL TO 1-(INHIBITOR OCCUPANCY FOR THAT ACTIVE SITE). THE RATIO OF INHIBITOR : GLYCEROL OCCUPANCY FOR EACH ACTIVE SITE WAS DETERMINED BY OCCUPANCY REFINEMENT IN CNS. THE AROMATIC RING OF EACH INHIBITOR AND THE NEARBY SIDE CHAIN OF LYS 32 SEEM TO SHOW SOME DISORDER (ESPECIALLY THE INHIBITOR AROMATIC RING). THE COORDINATES INDICATE TOO SHORT A DISTANCE BETWEEN LYS 32 IN CHAIN C AND THE AROMATIC RING OF THE NEARBY INHIBITOR. HOWEVER, THEIR AVERAGE POSITIONS DO NOT NECESSARILY REFLECT THEIR PROXIMITY AT ANY GIVEN TIME, DUE TO THIS DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 848 -random
Rwork0.198 ---
obs0.198 40990 99.7 %-
Displacement parametersBiso mean: 23.844 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.75→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 111 260 2958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.75-1.790.31490.30223502399
1.79-1.830.282500.27724892539
1.83-1.880.228530.23524902543
1.88-1.930.243630.21224392502
1.93-1.980.272450.21124912536
1.98-2.050.231540.19225192573
2.05-2.120.159560.17924872543
2.12-2.20.2400.19724852525
2.2-2.310.206520.20225082560
2.31-2.430.207560.20224982554
2.43-2.580.286600.20725042564
2.58-2.780.204430.20525282571
2.78-3.060.208670.19925282595
3.06-3.50.164500.17825582608
3.5-4.410.155630.16525502613
4.41-1000.216470.20927182765

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