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Open data
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Basic information
Entry | Database: PDB / ID: 5jjg | ||||||
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Title | Structure of magnesium-loaded ALG-2 | ||||||
![]() | Pcalcium-binding protein ALG-2, rogrammed cell death protein 6 | ||||||
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Function / homology | ![]() neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / endoplasmic reticulum exit site ...neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / endoplasmic reticulum exit site / ubiquitin-like ligase-substrate adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum to Golgi vesicle-mediated transport / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanner, J.J. | ||||||
![]() | ![]() Title: EF5 Is the High-Affinity Mg(2+) Site in ALG-2. Authors: Tanner, J.J. / Frey, B.B. / Pemberton, T. / Henzl, M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 64.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zndS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19950.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 39-32% isopropanol, 0.10 M Tris, pH 7.4, 1.0 mM EGTA, 1.0 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 10, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection | Resolution: 1.72→54.35 Å / Num. obs: 22193 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.8 | |||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2ZND Resolution: 1.72→54.35 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 21.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.59 Å2 / Biso mean: 30.2269 Å2 / Biso min: 14.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.72→54.35 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: -13.71 Å / Origin y: 16.8607 Å / Origin z: -18.6279 Å
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Refinement TLS group | Selection details: chain A |