regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / response to type II interferon ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / response to type II interferon / negative regulation of DNA binding / DNA damage response, signal transduction by p53 class mediator / retinoic acid receptor signaling pathway / regulation of angiogenesis / SUMOylation of DNA damage response and repair proteins / type II interferon-mediated signaling pathway / response to retinoic acid / telomere maintenance / nuclear periphery / response to cytokine / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / protein dimerization activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function
Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily ...Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Method to determine structure: SAD / Resolution: 1.6→27.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.337 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19229
2950
5.1 %
RANDOM
Rwork
0.17303
-
-
-
all
0.17402
55205
-
-
obs
0.17402
55205
94.17 %
-
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: 25.806 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.6 Å2
0 Å2
0.38 Å2
2-
-
-0.3 Å2
-0 Å2
3-
-
-
0.67 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→27.72 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2866
0
32
200
3098
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.019
3038
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2826
X-RAY DIFFRACTION
r_angle_refined_deg
1.392
1.939
4088
X-RAY DIFFRACTION
r_angle_other_deg
0.804
3
6520
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.27
5
359
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.802
23.72
164
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.542
15
557
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.49
15
25
X-RAY DIFFRACTION
r_chiral_restr
0.083
0.2
416
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
3442
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
775
X-RAY DIFFRACTION
r_mcbond_it
1.564
1.914
1409
X-RAY DIFFRACTION
r_mcbond_other
1.556
1.912
1408
X-RAY DIFFRACTION
r_mcangle_it
2.504
2.856
1765
X-RAY DIFFRACTION
r_mcangle_other
2.505
2.858
1766
X-RAY DIFFRACTION
r_scbond_it
2.59
2.261
1629
X-RAY DIFFRACTION
r_scbond_other
2.589
2.261
1629
X-RAY DIFFRACTION
r_scangle_other
4.127
3.27
2320
X-RAY DIFFRACTION
r_long_range_B_refined
5.732
15.906
3624
X-RAY DIFFRACTION
r_long_range_B_other
5.689
15.541
3527
LS refinement shell
Resolution: 1.598→1.639 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.18
212
-
Rwork
0.184
3848
-
obs
-
-
89.55 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.3951
-0.2914
-0.0312
0.6138
-0.0411
0.2724
0.0726
0.0495
0.0044
-0.0094
-0.0698
0.0003
0.0251
-0.0093
-0.0028
0.0408
0.0187
-0.0034
0.0237
0.0007
0.0157
26.1287
3.8545
16.319
2
0.746
-0.0057
0.2432
0.2128
0.109
0.3342
0.11
0.0411
0.0471
-0.0274
-0.0722
-0.0682
-0.0153
-0.0703
-0.0377
0.0326
0.0344
0.0152
0.0565
0.0229
0.0283
-2.2987
24.0641
19.3789
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
701 - 878
2
X-RAY DIFFRACTION
2
B
701 - 875
+
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