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- PDB-8uqs: Crystal structure of the Opossum p53 tetramerization domain -

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Basic information

Entry
Database: PDB / ID: 8uqs
TitleCrystal structure of the Opossum p53 tetramerization domain
ComponentsCellular tumor antigen p53 (Fragment)
KeywordsTRANSCRIPTION / Opossum p53 tetramerization domain stability
Function / homology
Function and homology information


protein tetramerization / PML body / rhythmic process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / apoptotic process / endoplasmic reticulum / metal ion binding
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
Cellular tumor antigen p53
Similarity search - Component
Biological speciesMonodelphis domestica (gray short-tailed opossum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWahba, H.M. / Sakaguchi, S. / Nakagawa, N. / Wada, J. / Kamada, R. / Sakaguchi, K. / Omichinski, J.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2023-03837 Canada
CitationJournal: Int J Mol Sci / Year: 2023
Title: Highly Similar Tetramerization Domains from the p53 Protein of Different Mammalian Species Possess Varying Biophysical, Functional and Structural Properties.
Authors: Sakaguchi, S. / Nakagawa, N. / Wahba, H.M. / Wada, J. / Kamada, R. / Omichinski, J.G. / Sakaguchi, K.
History
DepositionOct 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellular tumor antigen p53 (Fragment)
B: Cellular tumor antigen p53 (Fragment)
C: Cellular tumor antigen p53 (Fragment)
D: Cellular tumor antigen p53 (Fragment)


Theoretical massNumber of molelcules
Total (without water)16,0544
Polymers16,0544
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-30 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.275, 50.887, 60.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
Cellular tumor antigen p53 (Fragment)


Mass: 4013.499 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monodelphis domestica (gray short-tailed opossum)
Gene: p53 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8HY32
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→32.31 Å / Num. obs: 24100 / % possible obs: 90.51 % / Redundancy: 5.6 % / CC1/2: 0.999 / Net I/σ(I): 12.46
Reflection shellResolution: 1.35→1.398 Å / Num. unique obs: 1080 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→32.31 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 1992 8.3 %
Rwork0.1688 --
obs0.1716 24002 90.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 0 133 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011122
X-RAY DIFFRACTIONf_angle_d1.0691498
X-RAY DIFFRACTIONf_dihedral_angle_d13.988454
X-RAY DIFFRACTIONf_chiral_restr0.069156
X-RAY DIFFRACTIONf_plane_restr0.013197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.4303470.3976551X-RAY DIFFRACTION32
1.38-1.420.3628960.33551044X-RAY DIFFRACTION61
1.42-1.460.33191250.25251363X-RAY DIFFRACTION80
1.46-1.510.28411440.19621598X-RAY DIFFRACTION93
1.51-1.560.21591520.18441677X-RAY DIFFRACTION99
1.56-1.630.21751560.17731722X-RAY DIFFRACTION100
1.63-1.70.24091560.15921722X-RAY DIFFRACTION100
1.7-1.790.17851560.14471729X-RAY DIFFRACTION100
1.79-1.90.20271550.1441717X-RAY DIFFRACTION100
1.9-2.050.17961580.14821743X-RAY DIFFRACTION100
2.05-2.260.19011590.13831752X-RAY DIFFRACTION100
2.26-2.580.17741570.15171743X-RAY DIFFRACTION100
2.58-3.250.18741610.16631777X-RAY DIFFRACTION100
3.25-32.310.20341700.1851872X-RAY DIFFRACTION100

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