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- PDB-1u2b: Triglycine variant of the Grp1 Pleckstrin Homology Domain unliganded -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u2b | ||||||
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Title | Triglycine variant of the Grp1 Pleckstrin Homology Domain unliganded | ||||||
![]() | Cytohesin 3 | ||||||
![]() | LIPID BINDING PROTEIN / PH domain / lipid binding / phosphoinositides | ||||||
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 | ![]() ![]() | ||||||
![]() | Cronin, T.C. / DiNitto, J.P. / Czech, M.P. / Lambright, D.G. | ||||||
![]() | ![]() Title: Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains Authors: Cronin, T.C. / DiNitto, J.P. / Czech, M.P. / Lambright, D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.5 KB | Display | ![]() |
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PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.3 KB | Display | ![]() |
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Full document | ![]() | 432.9 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u27C ![]() 1u29C ![]() 1fgyS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 16259.445 Da / Num. of mol.: 1 / Fragment: PH Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: PEG 4000, sodium acetate, 10% glycerol, lithium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 15937 / Num. obs: 15719 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.8→1.85 Å / % possible all: 96.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1FGY Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.746 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Hydrogens have been added in the riding positions. Several atoms for residues 280, 323, 334, 335, 336, 353, 355, 370 and 387 were modeled into this structure with zero occupancy because they ...Details: Hydrogens have been added in the riding positions. Several atoms for residues 280, 323, 334, 335, 336, 353, 355, 370 and 387 were modeled into this structure with zero occupancy because they are part of the PH domain and were not deleted or mutated.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20 /
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