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- PDB-3fwu: Crystal structure of Leishmania major MIF1 -

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Basic information

Entry
Database: PDB / ID: 3fwu
TitleCrystal structure of Leishmania major MIF1
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 / molecular replacement / Resolution: 1.8 Å
AuthorsRIchardson, J.M. / Walkinshaw, M.D.
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 24, 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)14,6981
Polymers14,6981
Non-polymers00
Water1,00956
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)44,0933
Polymers44,0933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6970 Å2
ΔGint-52 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.321, 52.321, 97.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Macrophage migration inhibitory factor-like protein


Mass: 14697.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LmjF33.1740 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q413
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.76 Å3/Da / Density % sol: 29.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% w/v PEG 4000, 100mM Imidazole, pH 6.5, Hanging drop, temperature 290K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9765 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 9160 / % possible obs: 98.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 7.2 / Num. unique all: 1242 / % possible all: 93.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UIZ

1uiz


Resolution: 1.8→21.54 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.85 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.264 439 4.8 %RANDOM
Rwork0.2 ---
obs0.203 9160 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.23 Å2 / Biso mean: 18.299 Å2 / Biso min: 9.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 56 946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022917
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9491256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7695118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56823.15838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58515143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.879155
X-RAY DIFFRACTIONr_chiral_restr0.0720.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021702
X-RAY DIFFRACTIONr_mcbond_it0.5871.5574
X-RAY DIFFRACTIONr_mcangle_it1.0922944
X-RAY DIFFRACTIONr_scbond_it1.8353343
X-RAY DIFFRACTIONr_scangle_it3.0184.5309
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 24 -
Rwork0.24 603 -
all-627 -
obs--90.74 %

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