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- PDB-1fhx: Structure of the pleckstrin homology domain from GRP1 in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fhx | ||||||
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Title | Structure of the pleckstrin homology domain from GRP1 in complex with inositol 1,3,4,5-tetrakisphosphate | ||||||
![]() | GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1 | ||||||
![]() | SIGNALING PROTEIN / PLECKSTRIN / 3-PHOSPHOINOSITIDES / INOSITOL TETRAKISPHOSPHATE SIGNAL TRANSDUCTION PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR | ||||||
Function / homology | ![]() Intra-Golgi traffic / Golgi vesicle transport / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of cell adhesion / bicellular tight junction / ruffle / guanyl-nucleotide exchange factor activity / adherens junction ...Intra-Golgi traffic / Golgi vesicle transport / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of cell adhesion / bicellular tight junction / ruffle / guanyl-nucleotide exchange factor activity / adherens junction / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferguson, K.M. / Kavran, J.M. / Sankaran, V.G. / Fournier, E. / Isakoff, S.J. / Skolnik, E.Y. / Lemmon, M.A. | ||||||
![]() | ![]() 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 | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 51.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 545.7 KB | Display | ![]() |
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Full document | ![]() | 553.5 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1faoC ![]() 1fb8C ![]() 1fhwSC S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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3 |
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Unit cell |
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Details | The biological assembly is a monomer constructed from chain A or chain B |
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Components
#1: Protein | Mass: 15360.092 Da / Num. of mol.: 2 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN Source method: isolated from a genetically manipulated source Details: COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.3 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 8000, SODIUM ACETATE, AMMONIUM SULFATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||||
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 QUANTUM 4 / Detector: CCD / Date: Sep 24, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 15962 / Num. obs: 15962 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.23 / % possible all: 90.2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Num. measured all: 31494 |
Reflection shell | *PLUS % possible obs: 90.2 % / Mean I/σ(I) obs: 4.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1FHW: GRP1 PH DOMAIN Resolution: 2.5→30.68 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 168309.6 / 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: 38.09 Å2 / ksol: 0.325 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / 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: 500 Å / σ(F): 0 / % reflection Rfree: 9.5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.341 / % reflection Rfree: 8.7 % / Rfactor Rwork: 0.288 |