- PDB-4e68: Unphosphorylated STAT3B core protein binding to dsDNA -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4.0E+68
Title
Unphosphorylated STAT3B core protein binding to dsDNA
Components
DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
Signal transducer and activator of transcription 3
Keywords
TRANSCRIPTION/DNA / SH2 Domain / Protein DNA Complex / Signal Transducer / Activator of Transcription / Duplex DNA / Nucleus / Cytosol / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information
STAT3 nuclear events downstream of ALK signaling / Interleukin-10 signaling / MET activates STAT3 / Interleukin-37 signaling / Signaling by ALK / PTK6 Activates STAT3 / Interleukin-21 signaling / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling ...STAT3 nuclear events downstream of ALK signaling / Interleukin-10 signaling / MET activates STAT3 / Interleukin-37 signaling / Signaling by ALK / PTK6 Activates STAT3 / Interleukin-21 signaling / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / Interleukin-15 signaling / Interleukin-20 family signaling / Interleukin-27 signaling / Interleukin-23 signaling / retinal rod cell differentiation / Interleukin-6 signaling / radial glial cell differentiation / Interleukin-35 Signalling / Downstream signal transduction / negative regulation of primary miRNA processing / Interleukin-7 signaling / Signaling by SCF-KIT / leptin-mediated signaling pathway / negative regulation of neuron migration / PKR-mediated signaling / T-helper 17 type immune response / negative regulation of hydrogen peroxide biosynthetic process / negative regulation of inflammatory response to wounding / primary miRNA binding / response to leptin / sexual reproduction / interleukin-11-mediated signaling pathway / regulation of feeding behavior / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / cellular response to interleukin-17 / interleukin-9-mediated signaling pathway / regulation of cellular response to hypoxia / interleukin-2-mediated signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / nuclear glucocorticoid receptor binding / negative regulation of stem cell differentiation / acetylation-dependent protein binding / interleukin-15-mediated signaling pathway / cellular response to leptin stimulus / astrocyte differentiation / postsynapse to nucleus signaling pathway / positive regulation of cytokine production involved in inflammatory response / negative regulation of glycolytic process / regulation of mitochondrial membrane permeability / positive regulation of vascular endothelial cell proliferation / temperature homeostasis / eating behavior / positive regulation of ATP biosynthetic process / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / cellular response to cytokine stimulus / somatic stem cell population maintenance / cell surface receptor signaling pathway via JAK-STAT / positive regulation of interleukin-10 production / cellular response to organic cyclic compound / regulation of multicellular organism growth / positive regulation of vascular endothelial growth factor production / growth hormone receptor signaling pathway via JAK-STAT / energy homeostasis / signaling adaptor activity / negative regulation of autophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / transforming growth factor beta receptor signaling pathway / positive regulation of erythrocyte differentiation / positive regulation of interleukin-1 beta production / response to cytokine / acute-phase response / positive regulation of interleukin-8 production / response to ischemia / Schaffer collateral - CA1 synapse / mRNA transcription by RNA polymerase II / modulation of chemical synaptic transmission / chromatin DNA binding / response to peptide hormone / defense response / cytokine-mediated signaling pathway / positive regulation of miRNA transcription / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / protein import into nucleus / positive regulation of angiogenesis / nuclear receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / response to estradiol / glucose homeostasis / regulation of cell population proliferation / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / sequence-specific DNA binding Similarity search - Function
STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding domain / STAT3, SH2 domain / : / Signal transducer and activator of transcription, linker domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain ...STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding domain / STAT3, SH2 domain / : / Signal transducer and activator of transcription, linker domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / SH2 domain / SHC Adaptor Protein / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / p53-like transcription factor, DNA-binding / EF-hand / Recoverin; domain 1 / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 2.585→14.98 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.223 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27332
1810
5 %
RANDOM
Rwork
0.22532
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obs
0.22778
34413
97.08 %
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all
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34413
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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: 68.881 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.01 Å2
Refinement step
Cycle: LAST / Resolution: 2.585→14.98 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4499
360
0
139
4998
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.019
4987
X-RAY DIFFRACTION
r_angle_refined_deg
1.732
1.911
6810
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
2.203
5
556
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
28.652
24.928
209
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.974
15
869
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.673
15
25
X-RAY DIFFRACTION
r_chiral_restr
0.126
0.2
750
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
3569
LS refinement shell
Resolution: 2.585→2.65 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.385
137
-
Rwork
0.361
2420
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obs
-
2420
99.22 %
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