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Yorodumi- PDB-1u2b: Triglycine variant of the Grp1 Pleckstrin Homology Domain unliganded -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u2b | ||||||
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Title | Triglycine variant of the Grp1 Pleckstrin Homology Domain unliganded | ||||||
Components | Cytohesin 3 | ||||||
Keywords | LIPID BINDING PROTEIN / PH domain / lipid binding / phosphoinositides | ||||||
Function / homology | Function and homology information Intra-Golgi traffic / regulation of ARF protein signal transduction / Golgi vesicle transport / establishment of epithelial cell polarity / 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 / regulation of ARF protein signal transduction / Golgi vesicle transport / establishment of epithelial cell polarity / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cronin, T.C. / DiNitto, J.P. / Czech, M.P. / Lambright, D.G. | ||||||
Citation | Journal: Embo J. / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u2b.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u2b.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 1u2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/1u2b ftp://data.pdbj.org/pub/pdb/validation_reports/u2/1u2b | HTTPS FTP |
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-Related structure data
Related structure data | 1u27C 1u29C 1fgyS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 16259.445 Da / Num. of mol.: 1 / Fragment: PH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pscd3, Grp1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O08967 | ||
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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: 2.73 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: ROTATING ANODE / Wavelength: 1.54 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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