SUMOylation of DNA damage response and repair proteins / G2/M DNA damage checkpoint / Nonhomologous End-Joining (NHEJ) / mitotic DNA damage checkpoint signaling / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA replication checkpoint signaling / regulation of autophagosome assembly / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling ...SUMOylation of DNA damage response and repair proteins / G2/M DNA damage checkpoint / Nonhomologous End-Joining (NHEJ) / mitotic DNA damage checkpoint signaling / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA replication checkpoint signaling / regulation of autophagosome assembly / protein localization to site of double-strand break / mitotic intra-S DNA damage checkpoint signaling / cell cycle / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / histone reader activity / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / positive regulation of transcription initiation by RNA polymerase II / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / G2/M DNA damage checkpoint / protein catabolic process / Regulation of TP53 Activity through Methylation / PML body / cellular response to gamma radiation / G2/M transition of mitotic cell cycle / Regulation of TP53 Degradation / chromosome / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / nuclear body / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / cell division / DNA repair / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / DNA damage response / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein kinase binding / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function
Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / BRCT domain, a BRCA1 C-terminus domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / breast cancer carboxy-terminal domain ...Regulator of Ty1 transposition protein 107 BRCT domain / Tumour Suppressor Smad4 - #20 / BRCT domain, a BRCA1 C-terminus domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta Similarity search - Domain/homology
Resolution: 1.54→1.6 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3039 / Rsym value: 0.508 / % possible all: 99.3
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SHELXS
phasing
REFMAC
5.6.0117
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.54→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.104 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20465
1546
5 %
RANDOM
Rwork
0.15925
-
-
-
all
0.1616
31042
-
-
obs
0.1616
29179
98.98 %
-
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: 23.648 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.91 Å2
0 Å2
-0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.92 Å2
Refinement step
Cycle: LAST / Resolution: 1.54→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1782
0
0
153
1935
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.019
1833
X-RAY DIFFRACTION
r_angle_refined_deg
2.293
1.987
2498
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.665
5
224
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.372
23.25
80
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.827
15
291
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.767
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.171
0.2
272
X-RAY DIFFRACTION
r_gen_planes_refined
0.015
0.022
1414
X-RAY DIFFRACTION
r_rigid_bond_restr
7.855
3
1833
X-RAY DIFFRACTION
r_sphericity_free
20.219
5
62
X-RAY DIFFRACTION
r_sphericity_bonded
13.584
5
1873
LS refinement shell
Resolution: 1.54→1.58 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.261
109
-
Rwork
0.18
1951
-
obs
-
-
98.71 %
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
1.0035
0.0097
0.3494
0.0132
-0.0939
1.1976
-0.0627
-0.0259
0.0818
0.0007
-0.0157
-0.0041
0.0369
0.0101
0.0784
0.0307
-0.0124
-0.008
0.0315
-0.0016
0.0114
19.3651
33.6512
26.1557
2
0.9025
0.1643
0.0262
0.4103
0.0129
0.5273
0.0005
-0.024
0.0076
-0.0565
-0.0063
-0.0373
-0.0255
-0.0169
0.0058
0.0119
0.0054
0.0077
0.0099
0.0017
0.0273
17.3051
36.3626
1.0532
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
27 - 137
2
X-RAY DIFFRACTION
1
A
201 - 263
3
X-RAY DIFFRACTION
2
B
28 - 135
4
X-RAY DIFFRACTION
2
B
201 - 279
+
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