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Yorodumi- PDB-4p2j: Crystal structure of the mouse SNX19 PX domain with bound sulphate ion -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p2j | ||||||
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Title | Crystal structure of the mouse SNX19 PX domain with bound sulphate ion | ||||||
Components | MKIAA0254 protein | ||||||
Keywords | SIGNALING PROTEIN / sorting nexin / phox homology domain | ||||||
Function / homology | Function and homology information dense core granule maturation / insulin secretion / exocytosis / chondrocyte differentiation / phosphatidylinositol binding / establishment of localization in cell / early endosome membrane / intracellular membrane-bounded organelle / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Collins, B.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural Basis for Different Phosphoinositide Specificities of the PX Domains of Sorting Nexins Regulating G-protein Signaling. Authors: Mas, C. / Norwood, S.J. / Bugarcic, A. / Kinna, G. / Leneva, N. / Kovtun, O. / Ghai, R. / Ona Yanez, L.E. / Davis, J.L. / Teasdale, R.D. / Collins, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p2j.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p2j.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 4p2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/4p2j ftp://data.pdbj.org/pub/pdb/validation_reports/p2/4p2j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15658.753 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx19, mKIAA0254 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80U53, UniProt: Q6P4T1*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG3350, 0.25 M NaCl, 5% glycerol, 0.1 M Tris (pH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray / Wavelength: 0.9537 |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→78.8 Å / Num. obs: 13235 / % possible obs: 99.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.4 |
Reflection shell | Mean I/σ(I) obs: 3.4 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.4→61.287 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→61.287 Å
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Refine LS restraints |
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LS refinement shell |
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