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- PDB-1eaz: Crystal structure of the phosphoinositol (3,4)-bisphosphate bindi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1eaz | ||||||
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Title | Crystal structure of the phosphoinositol (3,4)-bisphosphate binding PH domain of TAPP1 from human. | ||||||
![]() | TANDEM PH DOMAIN CONTAINING PROTEIN-1 | ||||||
![]() | LIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / LIPID DEGRADATION / ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomas, C.C. / Dowler, S. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
![]() | ![]() Title: Crystal Structure of the Phosphatidylinositol 3,4-Bisphosphate-Binding Pleckstrin Homology (Ph) Domain of Tandem Ph-Domain-Containing Protein 1 (Tapp1): Molecular Basis of Lipid Specificity Authors: Thomas, C.C. / Dowler, S. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. #1: Journal: Biochem.J. / Year: 2000 Title: Identification of Pleckstrin-Homology-Domain-Containing Proteins with Novel Phosphoinositide-Binding Specificities Authors: Dowler, S. / Currie, R.A. / Campbell, D.G. / Deak, M. / Kular, G. / Downes, C.P. / Alessi, D.R. #2: ![]() Title: Structural Basis for Discrimination of 3-Phosphoinositides by Pleckstrin Homology Domains Authors: Ferguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.1 KB | Display | ![]() |
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PDB format | ![]() | 47.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1fb8S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14240.303 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN RESIDUES 182-303 Source method: isolated from a genetically manipulated source Details: ORDERED CITRATE MOLECULE IN LIPID BINDING POCKET / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CIT / ![]() |
#3: Water | ChemComp-HOH / ![]() |
Sequence details | PROTEIN IS PH DOMAIN FROM ACCESSION NUMBER PROTEIN |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 5.6 Details: 0.085M SODIUM CITRATE, 25.5% PEG 4000, 15% GLYCEROL, 0.17M AMMONIUM ACETATE, pH 5.60 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 25, 2001 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→27.524 Å / Num. obs: 27661 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 4.2 / % possible all: 97.7 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 97.7 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1FB8 Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: MODEL BUILT WITH WARPNTRACE, REFINEMENT STARTED USING CNS THEN USED SHELXL USED ANISOTROPIC B-FACTORS IN SHELXL REFINEMENT.
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Refine analyze | Occupancy sum non hydrogen: 990 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rwork![]() | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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