+Open data
-Basic information
Entry | Database: PDB / ID: 6koj | ||||||
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Title | Crystal structure of SNX11-PXe domain in complex with PI(3,5)P2 | ||||||
Components | Sorting nexin-11 | ||||||
Keywords | PROTEIN TRANSPORT / sorting nexin / phox-homology domain | ||||||
Function / homology | Function and homology information phosphatidylinositol phosphate binding / vesicle organization / intracellular protein transport / endosome / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Xu, T. / Liu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6koj.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6koj.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 6koj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/6koj ftp://data.pdbj.org/pub/pdb/validation_reports/ko/6koj | HTTPS FTP |
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-Related structure data
Related structure data | 6koiC 6kokC 4ikbS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 16 - 141 / Label seq-ID: 10 - 135
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-Components
#1: Protein | Mass: 16948.146 Da / Num. of mol.: 2 / Fragment: PX domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNX11 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9Y5W9 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.15 % / Mosaicity: 1.48 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: 0.1 M NaAc pH 4.6, 2% v/v Tacsimate pH 4.0, 16% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.14→45.27 Å / Num. obs: 12451 / % possible obs: 89.6 % / Redundancy: 3.2 % / CC1/2: 0.981 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.064 / Rrim(I) all: 0.118 / Net I/σ(I): 8.1 / Num. measured all: 40277 / Scaling rejects: 85 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IKB Resolution: 2.14→45.27 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.659 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.395 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 112.03 Å2 / Biso mean: 26.482 Å2 / Biso min: 9.46 Å2
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Refinement step | Cycle: final / Resolution: 2.14→45.27 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3906 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.143→2.199 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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