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- PDB-3fwt: Crystal structure of Leishmania major MIF2 -

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Basic information

Entry
Database: PDB / ID: 3fwt
TitleCrystal structure of Leishmania major MIF2
ComponentsMacrophage migration inhibitory factor-like protein
KeywordsCYTOKINE / homotrimer / tautomerase
Function / homology
Function and homology information


phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / 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
L-dopachrome isomerase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWalkinshaw, M.D. / Richardson, J.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structures of Leishmania major orthologues of macrophage migration inhibitory factor
Authors: Richardson, J.M. / Morrison, L.S. / Bland, N.D. / Bruce, S. / Coombs, G.H. / Mottram, J.C. / Walkinshaw, M.D.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor-like protein


Theoretical massNumber of molelcules
Total (without water)14,7701
Polymers14,7701
Non-polymers00
Water1,62190
1
A: Macrophage migration inhibitory factor-like protein

A: Macrophage migration inhibitory factor-like protein

A: Macrophage migration inhibitory factor-like protein


Theoretical massNumber of molelcules
Total (without water)44,3093
Polymers44,3093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6720 Å2
ΔGint-45 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.963, 53.963, 138.902
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-115-

HOH

21A-147-

HOH

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Components

#1: Protein Macrophage migration inhibitory factor-like protein


Mass: 14769.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LmjF33.1750 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q412
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 29% w/v PEG4000 and 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→38.8 Å / Num. all: 10155 / Num. obs: 10155 / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0066refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UIZ

1uiz


Resolution: 1.9→34.73 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.874 / SU B: 4.056 / SU ML: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.28 488 4.8 %
Rwork0.222 --
obs0.225 10072 99.5 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 22.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 0 90 993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022928
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.951259
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8895115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01923.15838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51315149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.937155
X-RAY DIFFRACTIONr_chiral_restr0.2120.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021711
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_it1.3551.5581
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2142937
X-RAY DIFFRACTIONr_scbond_it3.3353347
X-RAY DIFFRACTIONr_scangle_it4.844.5322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.365 33 -
Rwork0.369 689 -
obs--98.77 %

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