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Open data
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Basic information
Entry | Database: PDB / ID: 6kok | ||||||
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Title | Crystal Structure of SNX11/SNX10-PXe Chimera | ||||||
![]() | Sorting nexin-11,Uncharacterized protein SNX10 | ||||||
![]() | PROTEIN TRANSPORT / sorting nexin / phox-homology domain | ||||||
Function / homology | ![]() apical cytoplasm / extrinsic component of endosome membrane / tooth eruption / gastric acid secretion / 1-phosphatidylinositol binding / phosphatidylinositol phosphate binding / bone mineralization involved in bone maturation / vesicle organization / ruffle assembly / endosome organization ...apical cytoplasm / extrinsic component of endosome membrane / tooth eruption / gastric acid secretion / 1-phosphatidylinositol binding / phosphatidylinositol phosphate binding / bone mineralization involved in bone maturation / vesicle organization / ruffle assembly / endosome organization / cellular homeostasis / protein localization to cilium / protein localization to centrosome / cilium assembly / calcium ion homeostasis / bone resorption / phosphatidylinositol binding / osteoclast differentiation / secretory granule / cellular response to leukemia inhibitory factor / intracellular protein transport / endocytosis / ATPase binding / endosome / centrosome / endoplasmic reticulum / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, T. / Liu, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular Basis for PI(3,5)P2Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation. Authors: Xu, T. / Gan, Q. / Wu, B. / Yin, M. / Xu, J. / Shu, X. / 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 | ![]() | 81.3 KB | Display | ![]() |
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PDB format | ![]() | 58.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.6 KB | Display | ![]() |
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Full document | ![]() | 431.6 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6koiC ![]() 6kojC ![]() 4ikbS C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18744.201 Da / Num. of mol.: 2 / Fragment: SNX11/SNX10-PXe Chimera Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y5W9, UniProt: Q75MY3, UniProt: Q9Y5X0*PLUS #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % / Mosaicity: 0.77 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 / Details: 2.2 M NaCl, 0.1 M NaAc pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→47.91 Å / Num. obs: 21816 / % possible obs: 97 % / Redundancy: 3.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4IKB Resolution: 2→43.53 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 24.37 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.43 Å2 / Biso mean: 10.0853 Å2 / Biso min: 0.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→43.53 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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