protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria ...protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / NAD+ binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / 14-3-3 protein binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Crystals were obtained from 1:1 mix of protein and the well solution (9.5% (w/v) PEG3350, 100 mM CHES buffer), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution: 1.8→30.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.722 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2101
1430
5 %
RANDOM
Rwork
0.16493
-
-
-
obs
0.16715
26911
99.82 %
-
all
-
28402
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 16.398 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.63 Å2
0 Å2
-0 Å2
2-
-
0.21 Å2
0 Å2
3-
-
-
-0.84 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→30.01 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1958
0
1
247
2206
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.02
0.022
2092
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1470
X-RAY DIFFRACTION
r_angle_refined_deg
1.612
1.989
2839
X-RAY DIFFRACTION
r_angle_other_deg
0.951
3
3616
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.757
5
274
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.892
24.301
93
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.696
15.012
402
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.086
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.115
0.2
325
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
2306
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
408
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.19
1.5
1285
X-RAY DIFFRACTION
r_mcbond_other
0.443
1.5
517
X-RAY DIFFRACTION
r_mcangle_it
1.828
2
2094
X-RAY DIFFRACTION
r_scbond_it
2.869
3
807
X-RAY DIFFRACTION
r_scangle_it
4.117
4.5
731
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.799→1.846 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.282
104
-
Rwork
0.235
1931
-
obs
-
-
98.74 %
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
1.6918
-0.419
1.7289
3.3626
1.2053
5.6811
-0.0871
0.0828
0.1569
-0.2668
-0.002
-0.0493
-0.4401
0.253
0.0891
0.1278
-0.0109
0.0023
0.0414
-0.0179
0.0637
-4.595
36.557
14.382
2
1.6503
-0.4182
-0.057
1.675
-0.2661
2.634
-0.0281
0.0073
-0.1013
0.0078
-0.0086
-0.04
0.1435
0.0092
0.0367
0.0192
-0.0093
-0.0002
0.0232
-0.0023
0.0409
2.836
9.527
10.236
3
4.2001
0.2941
-1.5811
9.1463
1.7384
26.8497
-0.309
-0.8774
-0.2533
1.0673
0.1701
-0.3801
1.1522
1.0653
0.1389
0.3025
0.1222
-0.0316
0.2165
0.038
0.146
4.84
21.331
29.914
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
43 - 74
2
X-RAY DIFFRACTION
1
A
119 - 163
3
X-RAY DIFFRACTION
2
A
1 - 33
4
X-RAY DIFFRACTION
2
A
76 - 117
5
X-RAY DIFFRACTION
2
A
165 - 246
6
X-RAY DIFFRACTION
3
D
2 - 14
+
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