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- PDB-4p7s: Crystal structure of PfMIF in complex with 4-(3-methoxy-5-methylp... -

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Basic information

Entry
Database: PDB / ID: 4p7s
TitleCrystal structure of PfMIF in complex with 4-(3-methoxy-5-methylphenoxy)-2-(4-methoxyphenyl)-6-methylpyridine
ComponentsMacrophage migration inhibitory factor-like protein
KeywordsCYTOKINE/INHIBITOR / inhibitor / malaria complex active site / CYTOKINE-INHIBITOR complex
Function / homology
Function and homology information


phenylpyruvate tautomerase / L-dopachrome isomerase
Similarity search - Function
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
Chem-2OK / L-dopachrome isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.87 Å
AuthorsPantouris, G. / Lolis, E.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Crystallographic and Receptor Binding Characterization of Plasmodium falciparum Macrophage Migration Inhibitory Factor Complexed to Two Potent Inhibitors.
Authors: Pantouris, G. / Rajasekaran, D. / Garcia, A.B. / Ruiz, V.G. / Leng, L. / Jorgensen, W.L. / Bucala, R. / Lolis, E.J.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Oct 14, 2015Group: Data collection
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-like protein
B: Macrophage migration inhibitory factor-like protein
C: Macrophage migration inhibitory factor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6695
Polymers37,9993
Non-polymers6712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-14 kcal/mol
Surface area13550 Å2
MethodPISA
2
A: Macrophage migration inhibitory factor-like protein
B: Macrophage migration inhibitory factor-like protein
C: Macrophage migration inhibitory factor-like protein
hetero molecules

A: Macrophage migration inhibitory factor-like protein
B: Macrophage migration inhibitory factor-like protein
C: Macrophage migration inhibitory factor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,33910
Polymers75,9976
Non-polymers1,3424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area11770 Å2
ΔGint-42 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.554, 80.138, 97.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Macrophage migration inhibitory factor-like protein


Mass: 12666.221 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q3H7
#2: Chemical ChemComp-2OK / 4-(3-methoxy-5-methylphenoxy)-2-(4-methoxyphenyl)-6-methylpyridine


Mass: 335.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21NO3

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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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2 M ammonium sulphate, 0.1 M NaCl, 0.1 M Tris.HCl pH 8.0

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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: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 7288 / % possible obs: 98.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.059 / Χ2: 0.889 / Net I/av σ(I): 24.537 / Net I/σ(I): 12.4 / Num. measured all: 38798
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.88-2.934.80.4163240.695.9
2.93-2.985.30.3263771.776100
2.98-3.045.30.3743501.143100
3.04-3.15.40.2423710.904100
3.1-3.175.40.2033570.762100
3.17-3.245.50.1813760.68100
3.24-3.325.40.1533520.687100
3.32-3.415.50.1263680.634100
3.41-3.515.40.0913610.644100
3.51-3.635.40.0843640.609100
3.63-3.765.50.0743700.86599.7
3.76-3.915.50.0563590.65799.7
3.91-4.095.40.0513650.81799.2
4.09-4.35.40.043580.69998.9
4.3-4.575.30.0453661.35697.6
4.57-4.925.30.0323710.74396.9
4.92-5.425.40.0333700.85698.4
5.42-6.25.30.0323750.60999.7
6.2-7.815.20.0263830.60999.5
7.81-504.60.0263712.34289.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→48.83 Å / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Fo:Fc free: 0.773 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3451 334 4.6 %RANDOM
Rwork0.2869 6936 --
obs0.2896 7270 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.36 Å2 / Biso mean: 45.131 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2--0.17 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2.87→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 50 0 2136
Biso mean--41.42 --
Num. residues----297
LS refinement shellResolution: 2.875→2.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 28 -
Rwork0.308 473 -
all-501 -
obs--97.09 %

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