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

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Basic information

Entry
Database: PDB / ID: 2wkb
TitleCrystal Structure of Macrophage Migration Inhibitory Factor from Plasmodium berghei
ComponentsMACROPHAGE MIGRATION INHIBITORY FACTOR
KeywordsCYTOKINE
Function / homologyMacrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesPLASMODIUM BERGHEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 Inhibition Factor (Mif) 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 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
D: MACROPHAGE MIGRATION INHIBITORY FACTOR
E: MACROPHAGE MIGRATION INHIBITORY FACTOR
F: MACROPHAGE MIGRATION INHIBITORY FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,39614
Polymers84,6596
Non-polymers7378
Water8,863492
1
D: MACROPHAGE MIGRATION INHIBITORY FACTOR
E: MACROPHAGE MIGRATION INHIBITORY FACTOR
F: MACROPHAGE MIGRATION INHIBITORY FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6066
Polymers42,3303
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-21.3 kcal/mol
Surface area14850 Å2
MethodPISA
2
A: MACROPHAGE MIGRATION INHIBITORY FACTOR
B: MACROPHAGE MIGRATION INHIBITORY FACTOR
C: MACROPHAGE MIGRATION INHIBITORY FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7908
Polymers42,3303
Non-polymers4605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-18 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.703, 69.169, 80.217
Angle α, β, γ (deg.)90.00, 118.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9979, -0.0204, 0.0621), (0.0199, 0.9998, 0.0088), (-0.0623, -0.0075, 0.998)
Vector: 39.323, 31.052, 0.043)

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Components

#1: Protein
MACROPHAGE MIGRATION INHIBITORY FACTOR


Mass: 14109.884 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-116
Source method: isolated from a genetically manipulated source
Details: CYS2 IS MODIFIED TO CME IN ALL CHAINS DUE TO BINDING TO BETA-MERCAPTOETHANOL
Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote) / Strain: ANKA / Plasmid: PQE-70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q4YQW0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsS,S-(2-HYDROXYETHYL)THIOCYSTEINE (CME): BETA MERCAPTOETHANOL IS COVALENTLY BOUND TO CYS2 VIA A ...S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CME): BETA MERCAPTOETHANOL IS COVALENTLY BOUND TO CYS2 VIA A DISULPHIDE LINKAGE

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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: 2.24 Å3/Da / Density % sol: 45.06 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS-HCL PH 8.5, 13% PEG 6000, 0.2 M KSCN

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2008 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 72962 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.35
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.36 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OS5

2os5


Resolution: 1.78→70.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.872 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25455 3657 5 %RANDOM
Rwork0.19914 ---
obs0.2019 68813 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.256 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.2 Å2
2---0.57 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.78→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5309 0 48 492 5849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225560
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.9777492
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8475694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53824.38258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82615947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4541535
X-RAY DIFFRACTIONr_chiral_restr0.1540.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214155
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_it1.4371.53413
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.57725526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.57532147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6034.51957
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: 1.779→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 273 -
Rwork0.361 4833 -
obs--95.1 %

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