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- PDB-8uqt: Crystal structure of the Tree Shrew p53 tetramerization domain -

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Basic information

Entry
Database: PDB / ID: 8uqt
TitleCrystal structure of the Tree Shrew p53 tetramerization domain
ComponentsCellular tumor antigen p53
KeywordsTRANSCRIPTION / Tree Shrew 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 transactivation domain / P53 transactivation motif / 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 speciesTupaia chinensis (Chinese tree shrew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8553
Polymers7,7592
Non-polymers961
Water1,78399
1
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)15,7106
Polymers15,5184
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area7230 Å2
ΔGint-78 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.871, 65.806, 32.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-512-

HOH

31A-527-

HOH

41A-546-

HOH

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Components

#1: Protein/peptide Cellular tumor antigen p53


Mass: 3879.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tupaia chinensis (Chinese tree shrew) / Production host: Escherichia coli (E. coli) / References: UniProt: W8FSP6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.6 M Lithium sulfate monohydrate, 2% PEG 8000, 10% glycerol

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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: 1.16→45.46 Å / Num. obs: 21880 / % possible obs: 91.7 % / Redundancy: 9.9 % / CC1/2: 1 / Net I/σ(I): 28.35
Reflection shellResolution: 1.16→1.201 Å / Num. unique obs: 21822 / CC1/2: 0.84

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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: 1.16→45.46 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 2005 9.16 %
Rwork0.1716 --
obs0.1732 21880 91.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.16→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 5 99 640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009544
X-RAY DIFFRACTIONf_angle_d1.154721
X-RAY DIFFRACTIONf_dihedral_angle_d12.925215
X-RAY DIFFRACTIONf_chiral_restr0.08274
X-RAY DIFFRACTIONf_plane_restr0.01195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.190.4061610.4228547X-RAY DIFFRACTION36
1.19-1.220.3379930.2717949X-RAY DIFFRACTION62
1.22-1.250.24041190.19371252X-RAY DIFFRACTION82
1.25-1.290.21021510.16391472X-RAY DIFFRACTION95
1.29-1.340.20541480.15571532X-RAY DIFFRACTION99
1.34-1.390.20491630.16441520X-RAY DIFFRACTION100
1.39-1.460.1761490.13661546X-RAY DIFFRACTION100
1.46-1.530.1551590.12461551X-RAY DIFFRACTION100
1.53-1.630.15051620.12951550X-RAY DIFFRACTION100
1.63-1.760.17071550.14111569X-RAY DIFFRACTION100
1.76-1.930.16171550.14821553X-RAY DIFFRACTION100
1.93-2.210.1681590.14711573X-RAY DIFFRACTION100
2.21-2.790.18071600.17231591X-RAY DIFFRACTION100
2.79-45.460.21161710.20981670X-RAY DIFFRACTION100

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