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Yorodumi- PDB-7jtx: the structural basis of PTEN regulation by multi-site phosphorylation -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jtx | ||||||||||||
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Title | the structural basis of PTEN regulation by multi-site phosphorylation | ||||||||||||
Components | Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN | ||||||||||||
Keywords | HYDROLASE / PTEN / phosphatase / cellular localization | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å | ||||||||||||
Authors | Park, E. / Dempsey, D.R. / Cole, P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jtx.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jtx.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jtx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/7jtx ftp://data.pdbj.org/pub/pdb/validation_reports/jt/7jtx | HTTPS FTP |
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-Related structure data
Related structure data | 7jukC 7julC 7jvxC 1d5rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 300 mM sodium cistrate tribasic, 20% PEG 3350 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.05→3.29 Å / Rmerge(I) obs: 1.561 / Num. unique obs: 10 / Rpim(I) all: 0.893 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.62 Å2 / Biso mean: 102.7851 Å2 / Biso min: 60.87 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.23→39.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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