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- PDB-7jtx: the structural basis of PTEN regulation by multi-site phosphorylation -

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Entry
Database: PDB / ID: 7jtx
Titlethe structural basis of PTEN regulation by multi-site phosphorylation
ComponentsPhosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
KeywordsHYDROLASE / PTEN / phosphatase / cellular localization
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsPark, E. / Dempsey, D.R. / Cole, P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA74305 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM130961 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM120855 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2021
Title: The structural basis of PTEN regulation by multi-site phosphorylation.
Authors: Dempsey, D.R. / Viennet, T. / Iwase, R. / Park, E. / Henriquez, S. / Chen, Z. / Jeliazkov, J.R. / Palanski, B.A. / Phan, K.L. / Coote, P. / Gray, J.J. / Eck, M.J. / Gabelli, S.B. / Arthanari, H. / Cole, P.A.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN


Theoretical massNumber of molelcules
Total (without water)42,3391
Polymers42,3391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.865, 111.865, 60.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN


Mass: 42338.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
References: protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase

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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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 300 mM sodium cistrate tribasic, 20% PEG 3350 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.05→56.01 Å / Num. obs: 6977 / % possible obs: 98.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 98.79 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.2
Reflection shellResolution: 3.05→3.29 Å / Rmerge(I) obs: 1.561 / Num. unique obs: 10 / Rpim(I) all: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D5R

1d5r


Resolution: 3.23→39.55 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 612 10.13 %
Rwork0.228 5430 -
obs0.2316 6042 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.62 Å2 / Biso mean: 102.7851 Å2 / Biso min: 60.87 Å2
Refinement stepCycle: final / Resolution: 3.23→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 0 0 2322
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.23-3.560.33391470.31931332147997
3.56-4.070.32021510.263413541505100
4.08-5.130.24311530.21311355150899
5.14-39.550.23951610.20081389155099

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