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- PDB-2wkf: Crystal Structure of Macrophage Migration Inhibitory Factor from ... -

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Basic information

Entry
Database: PDB / ID: 2wkf
TitleCrystal Structure of Macrophage Migration Inhibitory Factor from Plasmodium falciparum
Components(MACROPHAGE MIGRATION INHIBITORY FACTOR) x 2
KeywordsCYTOKINE
Function / homology
Function and homology information


Maurer's cleft / adhesion of symbiont to host cell surface via host glycoprotein / Neutrophil degranulation / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / symbiont-mediated evasion of host immune response / cytokine activity / symbiont-mediated suppression of host toll-like receptor signaling pathway ...Maurer's cleft / adhesion of symbiont to host cell surface via host glycoprotein / Neutrophil degranulation / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / symbiont-mediated evasion of host immune response / cytokine activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / oxidoreductase activity / host cell surface receptor binding / extracellular space / cytoplasm
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
L-dopachrome isomerase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDobson, S.E. / Augustijn, K.D. / Brannigan, J.A. / Dodson, E.J. / Waters, A.P. / Wilkinson, A.J.
CitationJournal: Protein Sci. / Year: 2009
Title: The crystal structures of macrophage migration inhibitory factor from Plasmodium falciparum and Plasmodium berghei.
Authors: Dobson, S.E. / Augustijn, K.D. / Brannigan, J.A. / Schnick, C. / Janse, C.J. / Dodson, E.J. / Waters, A.P. / Wilkinson, A.J.
History
DepositionJun 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Database references / Non-polymer description
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1414
Polymers27,9572
Non-polymers1842
Water1,49583
1
A: MACROPHAGE MIGRATION INHIBITORY FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0332
Polymers13,9411
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MACROPHAGE MIGRATION INHIBITORY FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1092
Polymers14,0171
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.291, 83.291, 83.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

21B-2018-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.262, -0.4478, -0.8549), (0.8456, 0.3204, -0.427), (0.4651, -0.8347, 0.2947)
Vector: -16.198, 0.735, 31.143)

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Components

#1: Protein MACROPHAGE MIGRATION INHIBITORY FACTOR / MACROPHAGE MIGRATION INHIBITORY FACTOR HOMOLOG / PUTATIVE


Mass: 13940.556 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PQE-70 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q8I5C5
#2: Protein MACROPHAGE MIGRATION INHIBITORY FACTOR / MACROPHAGE MIGRATION INHIBITORY FACTOR HOMOLOG / PUTATIVE


Mass: 14016.674 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-116
Source method: isolated from a genetically manipulated source
Details: CYS2 IS MODIFIED TO CME IN CHAIN B DUE TO BINDING TO BETA-MERCAPTOETHANOL
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PQE-70 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q8I5C5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.63 % / Description: NONE
Crystal growpH: 8
Details: 10% PEG 1000, 10% PEG 8000, 0.2 M KSCN, 0.1 M TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2006 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 12419 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 14.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 34.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WKB

2wkb


Resolution: 2.05→58.9 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.885 / SU B: 16.881 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.32057 587 4.9 %RANDOM
Rwork0.24943 ---
obs0.253 11459 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.002 Å2
Refinement stepCycle: LAST / Resolution: 2.05→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 12 83 1665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221603
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9592163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16325.76978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06815274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.906159
X-RAY DIFFRACTIONr_chiral_restr0.1250.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021199
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0541.51013
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86521635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0073590
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7264.5527
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.048→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 38 -
Rwork0.286 874 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9248-0.47150.01850.8603-0.44112.0523-0.0197-0.02920.05080.02810.0570.0965-0.1721-0.1523-0.03730.08140.0055-0.00520.0282-0.00940.0892-1.205516.82193.2877
20.47660.21740.4110.9204-0.21731.7111-0.00520.08570.06280.08710.0123-0.1094-0.07730.0223-0.00710.02690.0050.00690.06510.03380.1154-2.529821.5959-27.6914
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 105
2X-RAY DIFFRACTION2A1 - 101

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