- PDB-4evg: Crystal Structure of MIF L46A mutant -
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Open data
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Basic information
Entry
Database: PDB / ID: 4evg
Title
Crystal Structure of MIF L46A mutant
Components
Macrophage migration inhibitory factor
Keywords
ISOMERASE / Keto-enol 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
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.954 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2137
2344
5 %
RANDOM
Rwork
0.17758
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-
-
all
0.17938
44152
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-
obs
0.17938
44152
98.25 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 24.121 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.92 Å2
-0 Å2
0 Å2
2-
-
1.19 Å2
-0 Å2
3-
-
-
-0.27 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2589
0
20
260
2869
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.027
0.02
2683
X-RAY DIFFRACTION
r_angle_refined_deg
2.286
1.958
3657
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.957
5
345
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.623
24.359
117
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.533
15
408
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.393
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.177
0.2
406
X-RAY DIFFRACTION
r_gen_planes_refined
0.013
0.021
2061
X-RAY DIFFRACTION
r_rigid_bond_restr
9.685
3
2683
X-RAY DIFFRACTION
r_sphericity_free
14.847
5
88
X-RAY DIFFRACTION
r_sphericity_bonded
10.461
5
2810
LS refinement shell
Resolution: 1.694→1.738 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.352
134
-
Rwork
0.278
2628
-
obs
-
-
85.35 %
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