- PDB-2oow: MIF Bound to a Fluorinated OXIM Derivative -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2oow
Title
MIF Bound to a Fluorinated OXIM Derivative
Components
Macrophage migration inhibitory factor
Keywords
ISOMERASE / alternative ligand-binding modes
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 arachidonate 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 arachidonate 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 / negative regulation of protein metabolic process / prostaglandin biosynthetic 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 peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / protease binding / secretory granule lumen / 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 / Neutrophil degranulation / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function
Resolution: 1.75→100 Å / FOM work R set: 0.881 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: THE STATISTICS LISTED BY RESOLUTION SHELL ARE FROM THE LAST ROUND OF CNS REFINEMENT. MINOR MANUAL ADJUSTEMENTS WERE PERFORMED AFTERWARDS. THE OVERALL STATISTICS REPRESENT THE FINAL MODEL. ...Details: THE STATISTICS LISTED BY RESOLUTION SHELL ARE FROM THE LAST ROUND OF CNS REFINEMENT. MINOR MANUAL ADJUSTEMENTS WERE PERFORMED AFTERWARDS. THE OVERALL STATISTICS REPRESENT THE FINAL MODEL. INHIBITOR MOLECULES WERE MODELLED WITH PARTIAL OCCUPANCIES. GLYCEROL MOLECULES MODELLED IN THE SAME ACTIVE SITES AS INHIBITOR HAVE OCCUPANCIES WERE MODLLED AS HAVING OCCUPANCIES EQUAL TO 1-(INHIBITOR OCCUPANCY FOR THAT ACTIVE SITE). THE RATIO OF INHIBITOR : GLYCEROL OCCUPANCY FOR EACH ACTIVE SITE WAS DETERMINED BY OCCUPANCY REFINEMENT IN CNS. THE AROMATIC RING OF EACH INHIBITOR AND THE NEARBY SIDE CHAIN OF LYS 32 SEEM TO SHOW SOME DISORDER (ESPECIALLY THE INHIBITOR AROMATIC RING). THE COORDINATES INDICATE TOO SHORT A DISTANCE BETWEEN LYS 32 IN CHAIN C AND THE AROMATIC RING OF THE NEARBY INHIBITOR. HOWEVER, THEIR AVERAGE POSITIONS DO NOT NECESSARILY REFLECT THEIR PROXIMITY AT ANY GIVEN TIME, DUE TO THIS DISORDER.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.204
848
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random
Rwork
0.198
-
-
-
obs
0.198
40990
99.7 %
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Displacement parameters
Biso mean: 23.844 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.21 Å
0.2 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.16 Å
0.14 Å
Refinement step
Cycle: LAST / Resolution: 1.75→100 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2587
0
111
260
2958
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.008
X-RAY DIFFRACTION
c_angle_deg
1.3
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection obs
1.75-1.79
0.31
49
0.302
2350
2399
1.79-1.83
0.282
50
0.277
2489
2539
1.83-1.88
0.228
53
0.235
2490
2543
1.88-1.93
0.243
63
0.212
2439
2502
1.93-1.98
0.272
45
0.211
2491
2536
1.98-2.05
0.231
54
0.192
2519
2573
2.05-2.12
0.159
56
0.179
2487
2543
2.12-2.2
0.2
40
0.197
2485
2525
2.2-2.31
0.206
52
0.202
2508
2560
2.31-2.43
0.207
56
0.202
2498
2554
2.43-2.58
0.286
60
0.207
2504
2564
2.58-2.78
0.204
43
0.205
2528
2571
2.78-3.06
0.208
67
0.199
2528
2595
3.06-3.5
0.164
50
0.178
2558
2608
3.5-4.41
0.155
63
0.165
2550
2613
4.41-100
0.216
47
0.209
2718
2765
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