+Open data
-Basic information
Entry | Database: PDB / ID: 1fb8 | ||||||
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Title | STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH | ||||||
Components | DUAL ADAPTOR OF PHOSPHOTYROSINE AND 3-PHOSPHOINOSITIDES | ||||||
Keywords | SIGNALING PROTEIN / PLECKSTRIN / 3-PHOSPHOINOSITIDES / INOSITOL TETRAKISPHOSPHATE SIGNAL TRANSDUCTION PROTEIN / ADAPTOR PROTEIN | ||||||
Function / homology | Function and homology information phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / protein dephosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / phospholipid binding / signal transduction / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å | ||||||
Authors | Ferguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fb8.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fb8.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/1fb8 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/1fb8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 14805.023 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UN19 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 40.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3450, Ethylene Glycol, Ammonium Phosphate, Sodium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Feb 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 4973 / Num. obs: 4973 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.04 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.2 / Num. unique all: 717 / Rsym value: 0.14 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 17635 |
Reflection shell | *PLUS % possible obs: 81.3 % / Mean I/σ(I) obs: 5.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→35 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 708822.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.75 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 14.9 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 43.7 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.321 / % reflection Rfree: 14.2 % / Rfactor Rwork: 0.271 |