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 ...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 / 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 / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / response to salt stress Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal grow
Details: PROTEIN SOLUTION: 5 MG/ML PROTEIN IN 20 MM CITRATE BUFFER PH 6.1, 150 MM NACL, 10 MM DTT. CRYSTALLIZATION BUFFER: 26% (W/V) PEG 3350, 43 MM SODIUM ACETATE AND 100 MM HEPES, PH 7.5
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.212 Å / σ(F): 1.35 / Phase error: 34.69 / Stereochemistry target values: TWIN_LSQ_F Details: IN THE UNBOUND P53 DNA-BINDING DOMAIN, THE LYS120 SIDE CHAIN IS HIGHLY FLEXIBLE. SIMILARLY, THE SIDE CHAIN OF ACETYLATED LYS120 SHOWED A HIGH DEGREE OF FLEXIBILITY, AND THE LACK OF DEFINED ...Details: IN THE UNBOUND P53 DNA-BINDING DOMAIN, THE LYS120 SIDE CHAIN IS HIGHLY FLEXIBLE. SIMILARLY, THE SIDE CHAIN OF ACETYLATED LYS120 SHOWED A HIGH DEGREE OF FLEXIBILITY, AND THE LACK OF DEFINED ELECTRON DENSITY PREVENTED UNAMBIGUOUS MODELING OF THE ACETYLATED SIDE CHAIN.
Rfactor
Num. reflection
% reflection
Rfree
0.226
6156
6 %
Rwork
0.1744
-
-
obs
0.1768
101869
83.31 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.326 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-6.1068 Å2
0 Å2
-2.0096 Å2
2-
-
11.937 Å2
0 Å2
3-
-
-
-5.8302 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→42.212 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6056
0
4
644
6704
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.006
6221
X-RAY DIFFRACTION
f_angle_d
0.97
8451
X-RAY DIFFRACTION
f_dihedral_angle_d
15.91
2327
X-RAY DIFFRACTION
f_chiral_restr
0.064
924
X-RAY DIFFRACTION
f_plane_restr
0.004
1122
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9001-1.9328
0.3184
220
0.2607
4823
X-RAY DIFFRACTION
79
1.9328-1.968
0.2798
259
0.2569
4771
X-RAY DIFFRACTION
78
1.968-2.0058
0.2969
254
0.2439
4824
X-RAY DIFFRACTION
79
2.0058-2.0467
0.2886
267
0.231
4864
X-RAY DIFFRACTION
78
2.0467-2.0912
0.2581
288
0.2205
4725
X-RAY DIFFRACTION
78
2.0912-2.1399
0.2656
274
0.2177
4790
X-RAY DIFFRACTION
79
2.1399-2.1934
0.2617
255
0.2098
4804
X-RAY DIFFRACTION
79
2.1934-2.2527
0.2371
227
0.2073
4896
X-RAY DIFFRACTION
79
2.2527-2.3189
0.2594
230
0.2038
4910
X-RAY DIFFRACTION
80
2.3189-2.3938
0.2682
238
0.1925
4826
X-RAY DIFFRACTION
80
2.3938-2.4793
0.2362
275
0.1973
4848
X-RAY DIFFRACTION
79
2.4793-2.5785
0.2736
243
0.1938
4914
X-RAY DIFFRACTION
80
2.5785-2.6958
0.231
244
0.1859
4809
X-RAY DIFFRACTION
80
2.6958-2.8379
0.2489
288
0.1829
4828
X-RAY DIFFRACTION
79
2.8379-3.0155
0.2015
213
0.1663
4931
X-RAY DIFFRACTION
80
3.0155-3.2482
0.2119
268
0.157
4848
X-RAY DIFFRACTION
79
3.2482-3.5746
0.2065
250
0.1342
4855
X-RAY DIFFRACTION
80
3.5746-4.091
0.1707
282
0.1279
4787
X-RAY DIFFRACTION
78
4.091-5.1508
0.1776
229
0.1197
4566
X-RAY DIFFRACTION
75
5.1508-32.1185
0.2038
296
0.1542
5138
X-RAY DIFFRACTION
84
+
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