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- PDB-4cz7: Truncated tetramerization domain of zebrafish p53 (crystal form III) -

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Basic information

Entry
Database: PDB / ID: 4cz7
TitleTruncated tetramerization domain of zebrafish p53 (crystal form III)
ComponentsCELLULAR TUMOR ANTIGEN P53P53
KeywordsCELL CYCLE / TUMOR SUPPRESSOR / TRANSCRIPTION FACTOR PROTEIN EVOLUTION / DANIO RERIO
Function / homology
Function and homology information


regulation of oogenesis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Regulation of TP53 Activity through Association with Co-factors / Regulation of TP53 Activity through Methylation / G2/M Checkpoints / RUNX3 regulates CDKN1A transcription / PKR-mediated signaling / Ovarian tumor domain proteases ...regulation of oogenesis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Regulation of TP53 Activity through Association with Co-factors / Regulation of TP53 Activity through Methylation / G2/M Checkpoints / RUNX3 regulates CDKN1A transcription / PKR-mediated signaling / Ovarian tumor domain proteases / Oxidative Stress Induced Senescence / Oncogene Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Stabilization of p53 / epithelium development / The role of GTSE1 in G2/M progression after G2 checkpoint / Ub-specific processing proteases / programmed cell death involved in cell development / intestinal epithelial structure maintenance / hematopoietic stem cell homeostasis / epidermis morphogenesis / apoptotic process involved in blood vessel morphogenesis / negative regulation of cell division / retrotransposon silencing / regulation of double-strand break repair / apoptotic process involved in development / response to methylmercury / 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 / erythrocyte development / negative regulation of cell cycle / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / anatomical structure morphogenesis / positive regulation of cell cycle / response to UV / negative regulation of angiogenesis / intrinsic apoptotic signaling pathway / transforming growth factor beta receptor signaling pathway / DNA damage checkpoint signaling / promoter-specific chromatin binding / protein tetramerization / regulation of protein stability / autophagy / cellular senescence / positive regulation of neuron apoptotic process / regulation of cell population proliferation / cellular response to hypoxia / spermatogenesis / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / apoptotic process / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / identical protein binding / metal ion binding / nucleus / 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
PHOSPHATE ION / Cellular tumor antigen p53 / Cellular tumor antigen p53
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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
E: CELLULAR TUMOR ANTIGEN P53
F: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,17310
Polymers22,7966
Non-polymers3774
Water2,522140
1
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)15,4797
Polymers15,1974
Non-polymers2823
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-54.5 kcal/mol
Surface area7580 Å2
MethodPISA
2
E: CELLULAR TUMOR ANTIGEN P53
F: CELLULAR TUMOR ANTIGEN P53
hetero molecules

E: CELLULAR TUMOR ANTIGEN P53
F: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3876
Polymers15,1974
Non-polymers1902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area6800 Å2
ΔGint-41.4 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.734, 45.717, 55.486
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3799.270 Da / Num. of mol.: 6
Fragment: TRUNCATED TETRAMERIZATION DOMAIN, RESIDUES 302-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G1K2L5, UniProt: P79734*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
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: 1.8 M SODIUM/POTASSIUM PHOSPHATE, PH 5.0.

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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: 1.1→27.7 Å / Num. obs: 68831 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.5 / % possible all: 87.4

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→27.7 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.789 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16588 3456 5 %RANDOM
Rwork0.14298 ---
obs0.14415 65375 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.823 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.64 Å2
2--0.39 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.1→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 21 140 1702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191641
X-RAY DIFFRACTIONr_bond_other_d0.0010.021660
X-RAY DIFFRACTIONr_angle_refined_deg1.242.0292214
X-RAY DIFFRACTIONr_angle_other_deg0.68933836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7615202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90224.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.43115354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.481518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
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_it0.9720.973758
X-RAY DIFFRACTIONr_mcbond_other0.9690.972757
X-RAY DIFFRACTIONr_mcangle_it1.351.461943
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6041.364882
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_restr1.4833298
X-RAY DIFFRACTIONr_sphericity_free27.047532
X-RAY DIFFRACTIONr_sphericity_bonded7.65653395
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.157 244 -
Rwork0.131 4356 -
obs--85.6 %

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