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- PDB-4d1l: Tetramerization domain of zebrafish p53 (crystal form I) -

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Basic information

Entry
Database: PDB / ID: 4d1l
TitleTetramerization domain of zebrafish p53 (crystal form I)
ComponentsCELLULAR TUMOR ANTIGEN P53
KeywordsTRANSCRIPTION / P53 FAMILY / TUMOR SUPPRESSOR / TRANSCRIPTION FACTOR / TETRAMER / PROTEIN EVOLUTION
Function / homology
Function and homology information


regulation of oogenesis / epidermis morphogenesis / hematopoietic stem cell homeostasis / negative regulation of cell division / apoptotic process involved in blood vessel morphogenesis / intestinal epithelial structure maintenance / transposable element silencing / response to methylmercury / definitive hemopoiesis / regulation of double-strand break repair ...regulation of oogenesis / epidermis morphogenesis / hematopoietic stem cell homeostasis / negative regulation of cell division / apoptotic process involved in blood vessel morphogenesis / intestinal epithelial structure maintenance / transposable element silencing / response to methylmercury / definitive hemopoiesis / regulation of double-strand break repair / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / erythrocyte maturation / negative regulation of cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / response to UV / erythrocyte development / positive regulation of cell cycle / transforming growth factor beta receptor signaling pathway / intrinsic apoptotic signaling pathway / DNA damage checkpoint signaling / negative regulation of angiogenesis / DNA damage response, signal transduction by p53 class mediator / protein tetramerization / regulation of protein stability / autophagy / cellular senescence / positive regulation of neuron apoptotic process / regulation of cell population proliferation / spermatogenesis / cellular response to hypoxia / sequence-specific DNA binding / transcription cis-regulatory region binding / positive regulation of apoptotic process / DNA-binding transcription factor activity / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
p53, subunit A / p53-like tetramerisation domain / : / 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, subunit A / p53-like tetramerisation domain / : / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Cellular tumor antigen p53
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
DepositionMay 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Structure summary
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3May 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 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)33,6438
Polymers33,5126
Non-polymers1312
Water97354
1
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)22,4075
Polymers22,3414
Non-polymers651
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-58.1 kcal/mol
Surface area9900 Å2
MethodPISA
2
A: CELLULAR TUMOR ANTIGEN P53
B: CELLULAR TUMOR ANTIGEN P53
hetero molecules

A: CELLULAR TUMOR ANTIGEN P53
B: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4726
Polymers22,3414
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7940 Å2
ΔGint-70.2 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.853, 120.611, 61.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 5585.328 Da / Num. of mol.: 6 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 302-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G1K2L5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP VAPOR DIFFUSION AT 20 DEGREE C; PROTEIN SOLUTION: 12 MG/ML IN 20 MM TRIS PH 7.5, 50 MM NACL, 5 MM DTT; CRYSTALLIZATION BUFFER: 50 MM ZINC ACETATE AND 20% (W/V) POLYETHYLENE GLYCOL 3,350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.97→28.5 Å / Num. obs: 23226 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.1
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C26

1c26


Resolution: 1.97→28.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.44 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24698 1164 5 %RANDOM
Rwork0.21731 ---
obs0.21876 22029 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.97→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 2 54 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191958
X-RAY DIFFRACTIONr_bond_other_d0.0010.021934
X-RAY DIFFRACTIONr_angle_refined_deg1.3422.0012624
X-RAY DIFFRACTIONr_angle_other_deg0.76434453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6415228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2424105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91315395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.931522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
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_it2.0433.233932
X-RAY DIFFRACTIONr_mcbond_other2.0423.234933
X-RAY DIFFRACTIONr_mcangle_it2.8044.8281157
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0163.7471026
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 81 -
Rwork0.272 1580 -
obs--98.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.4829-0.5679-3.17584.30391.30796.6865-0.16470.17590.09210.1623-0.06110.3252-0.2703-0.15870.22580.12650.0294-0.10960.0586-0.04860.1714-8.6907-24.293715.6849
27.6896-3.1143-2.025.37240.9022.8017-0.12460.38440.633-0.2164-0.0916-0.27-0.1692-0.21440.21610.1815-0.0405-0.11930.06250.04470.1621.8115-23.05316.6083
36.21993.077-2.12963.6003-1.50683.80780.1144-0.59910.19070.279-0.2030.0212-0.2510.37640.08860.1703-0.0286-0.06980.1218-0.02520.0922-19.9785-15.1352-7.0661
41.77760.1302-1.23065.7828-3.74846.63730.0171-0.1312-0.0221-0.1977-0.1624-0.18470.160.15690.14530.03330.0121-0.02960.0169-0.00820.1324-14.7052-11.8063-21.2892
53.72320.46740.47722.7396-1.24258.30040.1106-0.20210.11320.29720.09640.0732-0.1805-0.5849-0.2070.0756-0.00030.00990.0811-0.01660.1794-28.85-14.4042-9.841
65.37510.0433-3.36063.44660.47728.20610.09350.1360.2403-0.09330.09630.1198-0.3488-0.3308-0.18980.1380.0278-0.05850.02110.01870.1769-24.1862-8.2775-23.1853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A303 - 341
2X-RAY DIFFRACTION2B303 - 339
3X-RAY DIFFRACTION3C302 - 341
4X-RAY DIFFRACTION4D302 - 342
5X-RAY DIFFRACTION5E303 - 343
6X-RAY DIFFRACTION6F302 - 340

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