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Yorodumi- PDB-1fao: STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH IN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fao | ||||||
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Title | STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH IN COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 1fao.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fao.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fao_validation.pdf.gz | 462 KB | Display | wwPDB validaton report |
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Full document | 1fao_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 1fao_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1fao_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/1fao ftp://data.pdbj.org/pub/pdb/validation_reports/fa/1fao | HTTPS FTP |
-Related structure data
Related structure data | 1fb8SC 1fhwC 1fhxC 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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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 Details: COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UN19 |
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#2: Chemical | ChemComp-4IP / |
#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: 2.06 Å3/Da / Density % sol: 35 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3450, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: unknown | |||||||||||||||||||||||||
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: 1.8→50 Å / Num. all: 11260 / Num. obs: 11260 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 29 / Num. unique all: 966 / Rsym value: 0.05 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 50768 |
Reflection shell | *PLUS % possible obs: 99.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1FB8: UNLIGANDED DAPP1 Resolution: 1.8→30 Å / Rfactor Rfree error: 0.007 / 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: 40.12 Å2 / ksol: 0.398 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / 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: 30 Å / % reflection Rfree: 9.5 % / Rfactor obs: 0.219 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.5 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.277 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.226 |