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- PDB-7xvx: Neutron crystal structure of human macrophage migration inhibitor... -

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Basic information

Entry
Database: PDB / ID: 7xvx
TitleNeutron crystal structure of human macrophage migration inhibitory factor
ComponentsMacrophage migration inhibitory factor
KeywordsCYTOKINE / macrophage migration inhibitory factor / tautomerase
Function / homology
Function and homology information


positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEzawa, T. / Tamada, T. / Odaka, M. / Matsumura, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K07011 Japan
CitationJournal: To Be Published
Title: Neutron crystal structure of human macrophage migration inhibitory factor
Authors: Ezawa, T. / Nakagaki, T. / Sugishima, K. / Ishida, T. / Hirano, Y. / Kusaka, K. / Tamada, T. / Odaka, M. / Wakui, H. / Matsumura, H.
History
DepositionMay 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)37,0653
Polymers37,0653
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-44 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.534, 96.534, 105.596
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Macrophage migration inhibitory factor / MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / ...MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase


Mass: 12355.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.49 M Monosodium phosphate, 0.91 M Dipotassium phosphate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0313.05-5.47
SYNCHROTRONPhoton Factory BL-5A21
Detector
TypeIDDetectorDateDetails
iBIX1DIFFRACTOMETERJun 24, 2020The used detector is described in the paper (https://iopscience.iop.org/article/10.1088/1742-6596/528/1/012042/pdf).
DECTRIS PILATUS3 6M2PIXELOct 25, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
13.051
25.471
311
Reflection

Entry-ID: 7XVX

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Diffraction-IDNet I/σ(I)
1.6-48.277539499.91020.950.996214.7
2-203885399.46.60.98417.9
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.6-1.6336740.9232
2-2.1155890.4311

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
Refinement

SU ML: 0.1459 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 16.1419 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 7XTX

7xtx

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)Details
1.6-44.64X-RAY DIFFRACTION29.160.16920.15390.1547399371329753225.310021.93STARGazer used for data reduction is described in the paper (https://www.sciencedirect.com/science/article/abs/pii/S016890020801704X).
2-20NEUTRON DIFFRACTION0.20.183885399.41
Refinement stepCycle: LAST / Resolution: 1.6→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 0 215 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0416051
X-RAY DIFFRACTIONf_angle_d1.555810607
X-RAY DIFFRACTIONf_chiral_restr0.113433
X-RAY DIFFRACTIONf_plane_restr0.00741142
X-RAY DIFFRACTIONf_dihedral_angle_d19.18281582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.21571430.2132404X-RAY DIFFRACTION100
1.62-1.640.211410.19952448X-RAY DIFFRACTION100
1.64-1.660.2051390.20182435X-RAY DIFFRACTION100
1.66-1.680.24771410.2152440X-RAY DIFFRACTION100
1.68-1.70.25841430.22172437X-RAY DIFFRACTION100
1.7-1.730.27561440.21562404X-RAY DIFFRACTION100
1.73-1.750.20931400.21272419X-RAY DIFFRACTION100
1.75-1.780.23891400.20792455X-RAY DIFFRACTION100
1.78-1.810.20161400.19072433X-RAY DIFFRACTION100
1.81-1.840.20411360.18732417X-RAY DIFFRACTION100
1.84-1.880.20051420.1782451X-RAY DIFFRACTION100
1.88-1.910.17031420.16862423X-RAY DIFFRACTION100
1.91-1.950.19271410.16862448X-RAY DIFFRACTION100
1.95-1.990.18221410.16662443X-RAY DIFFRACTION100
1.99-2.040.17371350.16252448X-RAY DIFFRACTION100
2.04-2.090.16921320.1582442X-RAY DIFFRACTION100
2.09-2.150.14621320.15242464X-RAY DIFFRACTION100
2.15-2.210.17321330.15612445X-RAY DIFFRACTION100
2.21-2.280.19571370.1572457X-RAY DIFFRACTION100
2.28-2.360.16371350.1572466X-RAY DIFFRACTION100
2.36-2.460.17761360.15422457X-RAY DIFFRACTION100
2.46-2.570.17581310.16462474X-RAY DIFFRACTION100
2.57-2.70.18061320.15682464X-RAY DIFFRACTION100
2.71-2.870.17911340.15092486X-RAY DIFFRACTION100
2.87-3.10.17081330.15432497X-RAY DIFFRACTION100
3.1-3.410.13591330.14962498X-RAY DIFFRACTION100
3.41-3.90.15651360.12992499X-RAY DIFFRACTION100
3.9-4.910.12171390.10932528X-RAY DIFFRACTION100
4.91-44.640.16551420.15282647X-RAY DIFFRACTION99.89

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