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- PDB-4p7m: Crystal structure of Plasmodium falciparum MIF in complex with 3-... -

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Basic information

Entry
Database: PDB / ID: 4p7m
TitleCrystal structure of Plasmodium falciparum MIF in complex with 3-[(2-methyl-6-phenylpyridin-4-yl)oxy]phenol
ComponentsMacrophage migration inhibitory factor-like protein
KeywordsCYTOKINE/INHIBITOR / Malaria / inhibitor / active site / complex / CYTOKINE-INHIBITOR complex
Function / homology
Function and homology information


phenylpyruvate tautomerase / L-dopachrome isomerase / cytokine activity / extracellular space
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
3-[(2-methyl-6-phenylpyridin-4-yl)oxy]phenol / L-dopachrome isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.02 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 / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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-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)38,2764
Polymers37,9993
Non-polymers2771
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-14 kcal/mol
Surface area13400 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)76,5528
Polymers75,9976
Non-polymers5552
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area11760 Å2
ΔGint-43 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.036, 79.750, 97.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA1 - 1121 - 112
21SERSERBB1 - 1121 - 112
12ASPASPAA1 - 1011 - 101
22ASPASPCC1 - 1011 - 101
13ASPASPBB1 - 1011 - 101
23ASPASPCC1 - 1011 - 101

NCS ensembles :
ID
1
2
3

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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-2OE / 3-[(2-methyl-6-phenylpyridin-4-yl)oxy]phenol


Mass: 277.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15NO2

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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: 2.01 Å3/Da / Density % sol: 38.9 %
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: Sep 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. obs: 6087 / % possible obs: 96.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Χ2: 0.903 / Net I/av σ(I): 16.913 / Net I/σ(I): 13.5 / Num. measured all: 30549
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.02-3.075.10.3013121.35298.7
3.07-3.134.90.2543020.91299
3.13-3.1950.2313001.07699.3
3.19-3.255.10.2023050.79998.7
3.25-3.3250.1923080.80999.4
3.32-3.45.10.1632970.84199.3
3.4-3.494.90.1373100.88398.4
3.49-3.5850.133030.8599.7
3.58-3.6950.1243061.19198.4
3.69-3.850.1063060.99398.4
3.8-3.944.90.1043061.65298.7
3.94-4.15.20.0873040.99997.4
4.1-4.284.90.0782960.88897.4
4.28-4.5150.0723060.93696.2
4.51-4.7950.063090.79795.4
4.79-5.1650.062980.73695.8
5.16-5.685.10.0573120.61695.4
5.68-6.55.10.0512980.57795.5
6.5-8.195.10.0453050.53492.4
8.19-504.90.0493040.61885.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→25.02 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.829 / SU B: 26.923 / SU ML: 0.488 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.614
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3243 280 4.6 %RANDOM
Rwork0.2467 5797 --
obs0.2505 6077 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.25 Å2 / Biso mean: 48.283 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0 Å2
2--0.17 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 3.02→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 21 11 2123
Biso mean--87.76 31.97 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022169
X-RAY DIFFRACTIONr_bond_other_d0.0050.021883
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.952948
X-RAY DIFFRACTIONr_angle_other_deg1.1443.0024251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12925.86287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08215290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.57156
X-RAY DIFFRACTIONr_chiral_restr0.0730.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022568
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02505
X-RAY DIFFRACTIONr_mcbond_it3.6595.3091191
X-RAY DIFFRACTIONr_mcbond_other3.6555.3091190
X-RAY DIFFRACTIONr_mcangle_it5.8147.9381469
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A38260.11
12B38260.11
21A37180.13
22C37180.13
31B34070.12
32C34070.12
LS refinement shellResolution: 3.016→3.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 14 -
Rwork0.273 401 -
all-415 -
obs--91.61 %

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