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

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Basic information

Entry
Database: PDB / ID: 6lkv
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: 2.2 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
F: Macrophage migration inhibitory factor
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0797
Polymers62,9124
Non-polymers1673
Water7,638424
1
F: Macrophage migration inhibitory factor
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4045
Polymers47,2733
Non-polymers1322
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-62 kcal/mol
Surface area18810 Å2
MethodPISA
2
C: Macrophage migration inhibitory factor
hetero molecules

C: Macrophage migration inhibitory factor
hetero molecules

C: 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 operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7270 Å2
ΔGint-55 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.846, 110.846, 97.653
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11C-201-

CL

21C-373-

HOH

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Components

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

#1: Protein Macrophage migration inhibitory factor /


Mass: 15986.556 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: 15370.910 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: 15915.478 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: 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

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Non-polymers , 3 types, 427 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
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: 0.97849 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 35642 / % possible obs: 99.9 % / Redundancy: 20 % / CC star: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 55.25
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.473 / Num. unique obs: 1772 / CC star: 0.993

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BSI

5bsi


Resolution: 2.2→48.25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.026 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.191
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1782 5 %RANDOM
Rwork0.1795 ---
obs0.1818 33834 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 146.43 Å2 / Biso mean: 31.763 Å2 / Biso min: 13.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å2-0 Å2
2---0.08 Å20 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 2.2→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 7 424 4813
Biso mean--61.75 38.77 -
Num. residues----557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174219
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6356088
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5689760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27321.64250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55415783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0831536
X-RAY DIFFRACTIONr_chiral_restr0.0720.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02942
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.26 128 -
Rwork0.222 2469 -
obs--98.86 %

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