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- PDB-6lkw: Structural and functional insights into macrophage migration inhi... -

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Basic information

Entry
Database: PDB / ID: 6lkw
TitleStructural and functional insights into macrophage migration inhibitory factor from Oncomelania hupensis, the intermediate host of Schistosoma japonicum
Components(Macrophage migration inhibitory ...) x 4
KeywordsCYTOKINE / Oncomelania hupensis macrophage migration inhibitory factor / Isomerase / Beta-alpha-beta fold
Function / homologyphenylpyruvate tautomerase / L-dopachrome isomerase / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily / cytokine activity / extracellular space / L-dopachrome isomerase
Function and homology information
Biological speciesOncomelania hupensis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSu, Z.M. / Tian, X.Y. / Li, H.J. / Wei, Z.M. / Chen, L.F. / Ren, H.X. / Peng, W.F. / Tang, C.T.
CitationJournal: Biochem.J. / Year: 2020
Title: Structural and functional insights into macrophage migration inhibitory factor from Oncomelania hupensis, the intermediate host of Schistosoma japonicum.
Authors: Su, Z. / Tian, X. / Li, H. / Wei, Z. / Chen, L. / Wang, S. / Ren, H. / Peng, W. / Tang, C. / Lin, T. / Huang, S.
History
DepositionDec 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
D: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7476
Polymers61,6764
Non-polymers712
Water2,054114
1
A: Macrophage migration inhibitory factor
hetero molecules

A: Macrophage migration inhibitory factor
hetero molecules

A: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0246
Polymers46,9183
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area7180 Å2
ΔGint-56 kcal/mol
Surface area18000 Å2
MethodPISA
2
B: Macrophage migration inhibitory factor
D: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0724
Polymers46,0373
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-48 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.842, 172.842, 172.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-335-

HOH

31D-222-

HOH

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Components

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Macrophage migration inhibitory ... , 4 types, 4 molecules ABDC

#1: Protein Macrophage migration inhibitory factor /


Mass: 15639.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncomelania hupensis (invertebrata) / Gene: MIF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9W5E8
#2: Protein Macrophage migration inhibitory factor /


Mass: 15710.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncomelania hupensis (invertebrata) / Gene: MIF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9W5E8
#3: Protein Macrophage migration inhibitory factor /


Mass: 15299.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncomelania hupensis (invertebrata) / Gene: MIF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9W5E8
#4: Protein Macrophage migration inhibitory factor /


Mass: 15026.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncomelania hupensis (invertebrata) / Gene: MIF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9W5E8

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Non-polymers , 2 types, 116 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsIt may be sequencing errors or exist mutations of Oncomelania hupensis. From density map of ...It may be sequencing errors or exist mutations of Oncomelania hupensis. From density map of structure, it seems that residues of number 89, 90, 125 are correct.

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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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% (w/v) MPD, 0.1 M Sodium acetate (pH 4.6), and 20 mM Calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15176 / % possible obs: 100 % / Redundancy: 75.7 % / CC star: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 55.33
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 65.2 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 10 / Num. unique obs: 727 / CC star: 0.997 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BSI

5bsi


Resolution: 3.2→49.95 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.8 / SU B: 28.773 / SU ML: 0.477 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.6
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3331 735 4.9 %RANDOM
Rwork0.2303 ---
obs0.2352 14317 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.99 Å2 / Biso mean: 60.119 Å2 / Biso min: 7.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.2→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 2 114 4383
Biso mean--38.03 31.08 -
Num. residues----548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134342
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174098
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6375877
X-RAY DIFFRACTIONr_angle_other_deg1.2161.5679464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88321.646237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.33915751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8161536
X-RAY DIFFRACTIONr_chiral_restr0.0660.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024855
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02905
LS refinement shellResolution: 3.2→3.282 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.388 43 -
Rwork0.313 1021 -
obs--100 %

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