+Open data
-Basic information
Entry | Database: PDB / ID: 7f69 | ||||||
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Title | Crystal structure of WIPI2b in complex with ATG16L1 | ||||||
Components |
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Keywords | PROTEIN BINDING / WIPI2b / ATG16L1 | ||||||
Function / homology | Isoform 2 of Autophagy-related protein 16-1 / Isoform 2 of WD repeat domain phosphoinositide-interacting protein 2 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Gong, X.Y. / Pan, L.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2023 Title: ATG16L1 adopts a dual-binding site mode to interact with WIPI2b in autophagy. Authors: Gong, X. / Wang, Y. / Tang, Y. / Wang, Y. / Zhang, M. / Li, M. / Zhang, Y. / Pan, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f69.cif.gz | 214.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f69.ent.gz | 165 KB | Display | PDB format |
PDBx/mmJSON format | 7f69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f69_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 7f69_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 7f69_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 7f69_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/7f69 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/7f69 | HTTPS FTP |
-Related structure data
Related structure data | 7xfrC 5ltgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39002.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WIPI2, CGI-50 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4P8-2 |
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#2: Protein/peptide | Mass: 3796.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Production host: Escherichia coli (E. coli) / References: UniProt: Q676U5-2 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 42.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% w/v Pentaerythritol ethoxylate (15/4 EO/OH), 100 mM MES (pH 6.5), 50 mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→100 Å / Num. obs: 57102 / % possible obs: 98.43 % / Redundancy: 11.5 % / Biso Wilson estimate: 12.64 Å2 / Rmerge(I) obs: 0.232 / Net I/av σ(I): 9.7 / Net I/σ(I): 9.06 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 1.379 / Num. unique obs: 2848 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LTG Resolution: 1.5→28.8 Å / SU ML: 0.1442 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1959 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 20.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→28.8 Å
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Refine LS restraints |
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LS refinement shell |
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