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Yorodumi- PDB-1u27: Triglycine variant of the ARNO Pleckstrin Homology Domain in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u27 | ||||||
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Title | Triglycine variant of the ARNO Pleckstrin Homology Domain in complex with Ins(1,3,4,5)P4 | ||||||
Components | Cytohesin 2 | ||||||
Keywords | LIPID BINDING PROTEIN / Pleckstrin Homology domain / lipid binding / phosphoinositide | ||||||
Function / homology | Function and homology information extrinsic component of postsynaptic specialization membrane / Intra-Golgi traffic / negative regulation of dendrite development / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / ruffle / guanyl-nucleotide exchange factor activity / adherens junction ...extrinsic component of postsynaptic specialization membrane / Intra-Golgi traffic / negative regulation of dendrite development / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / ruffle / guanyl-nucleotide exchange factor activity / adherens junction / growth cone / postsynapse / glutamatergic synapse / lipid binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 1u27.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u27.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 1u27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/1u27 ftp://data.pdbj.org/pub/pdb/validation_reports/u2/1u27 | HTTPS FTP |
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-Related structure data
Related structure data | 1u29C 1u2bC 1fgyS 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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-Components
#1: Protein | Mass: 15054.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pscd2, Sec7b / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63034 |
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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: 2.3 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, sodium MES, 10% glycerol, pH 6.0, 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 5810 / Num. obs: 5810 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.3→2.37 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FGY Resolution: 2.3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Residues 377 and 388, and several atoms for residues 286, 298, 318, 331 and 336 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 | Bsol: 35.3169 Å2 / ksol: 0.306501 e/Å3 | ||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Xplor file |
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