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Open data
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Basic information
Entry | Database: PDB / ID: 4ikb | ||||||
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Title | Crystal structure of SNX11 PX domain | ||||||
![]() | (Sorting nexin- ...) x 2 | ||||||
![]() | PROTEIN TRANSPORT / SNX11 / PX domain | ||||||
Function / homology | ![]() phosphatidylinositol phosphate binding / vesicle organization / intracellular protein transport / endosome / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Xu, J. / Xu, T. / Liu, J. | ||||||
![]() | ![]() Title: Structure of Sorting Nexin 11 (SNX11) Reveals a Novel Extended PX Domain (PXe Domain) Critical for the Inhibition of Sorting Nexin 10 (SNX10) Induced Vacuolation Authors: Xu, J. / Xu, T. / Liu, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.7 KB | Display | ![]() |
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PDB format | ![]() | 56.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Sorting nexin- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 17156.113 Da / Num. of mol.: 1 / Fragment: PX domain, UNP residues 7-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 17112.248 Da / Num. of mol.: 1 / Fragment: PX domain, UNP residues 7-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 265 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/PE5.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PE5.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PE5 / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % / Mosaicity: 0.22 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.2M ammonium sulfate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30% PEG 8000, vapor diffusion, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.776→72.069 Å / Num. all: 27836 / Num. obs: 27836 / % possible obs: 97.4 % / Redundancy: 5.2 % / Rsym value: 0.064 / Net I/σ(I): 17.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.04 Å2 / Biso mean: 19.4674 Å2 / Biso min: 6.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→34.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.826 Å / Total num. of bins used: 20
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