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Yorodumi- PDB-5j68: Structure of Astrotactin-2, a conserved vertebrate-specific and p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j68 | |||||||||
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Title | Structure of Astrotactin-2, a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development | |||||||||
Components | Astrotactin-2 | |||||||||
Keywords | MEMBRANE PROTEIN / MACPF / annexin-like / fibronectin / neural guidance | |||||||||
Function / homology | Function and homology information establishment of body hair planar orientation / cell pole / inositol 1,3,4,5 tetrakisphosphate binding / neuron cell-cell adhesion / negative regulation of protein localization to cell surface / protein localization to cell surface / clathrin-coated vesicle / neuron migration / protein transport / late endosome ...establishment of body hair planar orientation / cell pole / inositol 1,3,4,5 tetrakisphosphate binding / neuron cell-cell adhesion / negative regulation of protein localization to cell surface / protein localization to cell surface / clathrin-coated vesicle / neuron migration / protein transport / late endosome / cell cortex / perikaryon / endosome / early endosome / calcium ion binding / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.221 Å | |||||||||
Authors | Ni, T. / Harlos, K. / Gilbert, R.J.C. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Open Biology / Year: 2016 Title: Structure of astrotactin-2: a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development. Authors: Ni, T. / Harlos, K. / Gilbert, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j68.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j68.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 5j68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j68_validation.pdf.gz | 899.5 KB | Display | wwPDB validaton report |
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Full document | 5j68_full_validation.pdf.gz | 905.4 KB | Display | |
Data in XML | 5j68_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 5j68_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/5j68 ftp://data.pdbj.org/pub/pdb/validation_reports/j6/5j68 | HTTPS FTP |
-Related structure data
Related structure data | 5j67SC 5j69C 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: 65054.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASTN2, KIAA0634 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O75129 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Chemical | ChemComp-I3P / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.31 Å3/Da / Density % sol: 80.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 5.0 to 6.0, 5% PEG 6000 / PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 5.22→85.802 Å / Num. obs: 6915 / % possible obs: 100 % / Redundancy: 23.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.3 |
Reflection shell | Highest resolution: 5.22 Å / Rmerge(I) obs: 3.047 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J67 Resolution: 5.221→85.802 Å / SU ML: 1.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 50.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.221→85.802 Å
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Refine LS restraints |
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LS refinement shell |
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