- PDB-4g83: Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a F... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4g83
Title
Crystal Structure of p73 DNA-Binding Domain Tetramer bound to a Full Response-Element
Components
Tumor protein p73
dna
Keywords
DNA BINDING PROTEIN/DNA / BETA-IMMUNOGLOBULIN FOLD / TUMOR SUPPRESSOR / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information
positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / mismatch repair / MDM2/MDM4 family protein binding / : / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function
Resolution: 4→45.61 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.887 / SU ML: 0.39 / Isotropic thermal model: TLS refinement / σ(F): 1.35 / Phase error: 28.13 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Rfree
0.3073
202
4.64 %
Rwork
0.2414
-
-
obs
0.2443
4349
99.82 %
all
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5072
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 68.022 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.48 Å2
0 Å2
0 Å2
2-
-
5.45 Å2
0 Å2
3-
-
-
-5.92 Å2
Refinement step
Cycle: LAST / Resolution: 4→45.61 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3094
410
2
0
3506
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.031
3640
X-RAY DIFFRACTION
f_angle_d
3.062
5032
X-RAY DIFFRACTION
f_dihedral_angle_d
20.914
1402
X-RAY DIFFRACTION
f_chiral_restr
0.1
552
X-RAY DIFFRACTION
f_plane_restr
0.014
594
LS refinement shell
Resolution: 4.0002→45.6125 Å
Rfactor
Num. reflection
% reflection
Rfree
0.3073
202
-
Rwork
0.2414
4147
-
obs
-
-
100 %
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
2.0375
-0.6919
1.0636
2.6688
-0.7298
1.8812
-0.2864
-0.0078
1.4485
-1.1429
0.4491
-0.3277
-0.1134
0.2876
0.5764
0.3483
0.3152
-0.0555
0.5483
0.5118
0.7995
-22.7571
-32.7521
9.3385
2
5.066
-0.4275
-2.3738
1.6489
0.9162
2.5592
-0.5233
0.4095
-0.5928
-0.5105
-0.2792
-0.1755
1.3492
0.0305
-0.2566
1.3344
0.166
0.0833
0.6077
0.0644
0.5611
-22.7099
-32.7407
8.032
3
2.168
1.1984
-0.4306
8.4996
-3.9227
2.8918
-0.542
0.2087
-0.4675
-0.674
-0.4141
-2.9198
0.1813
0.5368
-0.3165
0.1596
-0.257
-0.1057
0.3177
-0.0777
0.1433
-11.4072
-8.0051
13.2438
4
3.5469
-2.5135
-0.9597
7.3234
1.8799
2.981
-0.1748
-0.4719
-2.0314
1.7329
-0.3354
4.4161
-0.2336
-0.1539
0.0291
-0.0088
-0.0335
-0.4926
0.4532
-0.1318
-1.2789
-49.4701
-28.0807
3.7272
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
( CHAINEANDRESID400:409 )
E
400 - 409
2
X-RAY DIFFRACTION
2
( CHAINFANDRESID410:419 )
F
410 - 419
3
X-RAY DIFFRACTION
3
( CHAINAANDRESID1:310 )
A
1 - 310
4
X-RAY DIFFRACTION
4
( CHAINBANDRESID113:310 )
B
113 - 310
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