- PDB-1wu3: Crystal structure of recombinant murine interferon beta -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1wu3
Title
Crystal structure of recombinant murine interferon beta
Components
Interferon beta
Keywords
CYTOKINE / alpha-helix-bundle
Function / homology
Function and homology information
negative regulation of Lewy body formation / negative regulation of matrix metallopeptidase secretion / negative regulation of mononuclear cell migration / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / negative regulation of immunoglobulin production / Interferon alpha/beta signaling / natural killer cell activation involved in immune response / negative regulation of blood-brain barrier permeability / positive regulation of peptidyl-serine phosphorylation of STAT protein ...negative regulation of Lewy body formation / negative regulation of matrix metallopeptidase secretion / negative regulation of mononuclear cell migration / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / negative regulation of immunoglobulin production / Interferon alpha/beta signaling / natural killer cell activation involved in immune response / negative regulation of blood-brain barrier permeability / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of neuroinflammatory response / negative regulation of cell adhesion molecule production / positive regulation of transforming growth factor beta production / T cell activation involved in immune response / macrophage activation involved in immune response / cellular response to dsRNA / type I interferon-mediated signaling pathway / response to exogenous dsRNA / B cell proliferation / negative regulation of osteoclast differentiation / humoral immune response / negative regulation of type II interferon production / positive regulation of autophagy / cellular response to dexamethasone stimulus / B cell differentiation / cytokine activity / cellular response to virus / cytokine-mediated signaling pathway / neuron cellular homeostasis / defense response to virus / adaptive immune response / defense response to bacterium / negative regulation of cell population proliferation / extracellular space / extracellular region Similarity search - Function
#3: Journal: Pharmacol.Ther. / Year: 1993 Title: Structural, functional and evolutionary implications of the three-dimensional crystal structure of murine interferon-beta Authors: Mitsui, Y. / Senda, T. / Shimazu, T. / Matsuda, S. / Utsumi, J.
Method to determine structure: MIR / Resolution: 2.15→7.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.918 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24731
1182
10.1 %
RANDOM
Rwork
0.19162
-
-
-
all
0.1973
10525
-
-
obs
0.1973
10525
100 %
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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: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 38.011 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.25 Å2
0.12 Å2
0 Å2
2-
-
0.25 Å2
0 Å2
3-
-
-
-0.37 Å2
Refinement step
Cycle: LAST / Resolution: 2.15→7.95 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1394
0
0
48
1442
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
1412
X-RAY DIFFRACTION
r_angle_refined_deg
1.375
1.94
1899
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.181
5
159
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.763
23.553
76
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.054
15
283
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
26.3
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
208
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1044
X-RAY DIFFRACTION
r_nbd_refined
0.227
0.2
671
X-RAY DIFFRACTION
r_nbtor_refined
0.316
0.2
995
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.108
0.2
45
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.217
0.2
35
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.081
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
1.848
1.5
819
X-RAY DIFFRACTION
r_mcangle_it
2.425
2
1300
X-RAY DIFFRACTION
r_scbond_it
3.145
3
680
X-RAY DIFFRACTION
r_scangle_it
4.84
4.5
599
LS refinement shell
Resolution: 2.15→2.202 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.361
81
-
Rwork
0.345
604
-
obs
-
-
100 %
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