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- PDB-4cz6: Truncated tetramerization domain of zebrafish p53 (crystal form II) -

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Basic information

Entry
Database: PDB / ID: 4cz6
TitleTruncated tetramerization domain of zebrafish p53 (crystal form II)
ComponentsCELLULAR TUMOR ANTIGEN P53
KeywordsANTITUMOR PROTEIN / P53 FAMILY / TUMOR SUPPRESSOR / TRANSCRIPTION FACTOR / PROTEIN EVOLUTION
Function / homology
Function and homology information


regulation of oogenesis / Regulation of TP53 Expression / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Activity through Acetylation / Regulation of TP53 Activity through Association with Co-factors / Regulation of TP53 Activity through Methylation / RUNX3 regulates CDKN1A transcription / PKR-mediated signaling / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints ...regulation of oogenesis / Regulation of TP53 Expression / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Activity through Acetylation / Regulation of TP53 Activity through Association with Co-factors / Regulation of TP53 Activity through Methylation / RUNX3 regulates CDKN1A transcription / PKR-mediated signaling / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Ovarian tumor domain proteases / Ub-specific processing proteases / Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Degradation / Stabilization of p53 / The role of GTSE1 in G2/M progression after G2 checkpoint / epidermis morphogenesis / apoptotic process involved in blood vessel morphogenesis / programmed cell death involved in cell development / hematopoietic stem cell homeostasis / intestinal epithelial structure maintenance / negative regulation of cell division / response to methylmercury / transposable element silencing / apoptotic process involved in development / regulation of double-strand break repair / definitive hemopoiesis / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / erythrocyte maturation / negative regulation of cell cycle / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of cell cycle / erythrocyte development / response to UV / intrinsic apoptotic signaling pathway / negative regulation of angiogenesis / transforming growth factor beta receptor signaling pathway / DNA damage checkpoint signaling / promoter-specific chromatin binding / molecular condensate scaffold activity / protein tetramerization / regulation of protein stability / autophagy / positive regulation of neuron apoptotic process / cellular senescence / regulation of cell population proliferation / cellular response to hypoxia / spermatogenesis / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / metal ion binding / cytoplasm
Similarity search - Function
p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cellular tumor antigen p53
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsJoerger, A.C.
CitationJournal: Structure / Year: 2014
Title: Tracing the Evolution of the P53 Tetramerization Domain
Authors: Joerger, A.C. / Wilcken, R. / Andreeva, A.
History
DepositionApr 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULAR TUMOR ANTIGEN P53
B: CELLULAR TUMOR ANTIGEN P53
C: CELLULAR TUMOR ANTIGEN P53
D: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3035
Polymers15,1974
Non-polymers1061
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-39.5 kcal/mol
Surface area7110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.529, 57.529, 96.875
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11D-2003-

HOH

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Components

#1: Protein/peptide
CELLULAR TUMOR ANTIGEN P53 / TUMOR SUPPRESSOR P53 / P53


Mass: 3799.270 Da / Num. of mol.: 4
Fragment: TRUNCATED TETRAMERIZATION DOMAIN, RESIDUES 301-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P79734
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL GGS SEQUENCE AT THE N TERMINUS AS A RESULT OF CLONING STRATEGY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 17 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 50% (W/V) POLYETHYLENE GLYCOL 200, 100 MM TRIS, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8266
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.53→28.8 Å / Num. obs: 28720 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.8
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.53→49.82 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.786 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18365 1448 5 %RANDOM
Rwork0.14831 ---
obs0.15003 27232 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.936 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.53→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 7 72 1065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191018
X-RAY DIFFRACTIONr_bond_other_d0.0010.021031
X-RAY DIFFRACTIONr_angle_refined_deg1.12.0191361
X-RAY DIFFRACTIONr_angle_other_deg0.7332371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1625120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.32923.92956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29315217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9641513
X-RAY DIFFRACTIONr_chiral_restr0.0690.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2632.803476
X-RAY DIFFRACTIONr_mcbond_other2.2622.808477
X-RAY DIFFRACTIONr_mcangle_it2.684.211591
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9083.498542
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.00732048
X-RAY DIFFRACTIONr_sphericity_free25.5517
X-RAY DIFFRACTIONr_sphericity_bonded14.7652098
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 76 -
Rwork0.195 2036 -
obs--100 %

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