+Open data
-Basic information
Entry | Database: PDB / ID: 7y73 | ||||||
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Title | Crystal structure of sDscam Ig1 domain, isoform beta3v7 | ||||||
Components | Down Syndrome Cell Adhesion Molecules | ||||||
Keywords | CELL ADHESION / cell surface recptor | ||||||
Biological species | Chelicerata (chelicerates) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Chen, Q. / Yu, Y. / Cheng, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for the self-recognition of sDSCAM in Chelicerata. Authors: Cheng, J. / Yu, Y. / Wang, X. / Zheng, X. / Liu, T. / Hu, D. / Jin, Y. / Lai, Y. / Fu, T.M. / Chen, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y73.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y73.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 7y73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/7y73 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/7y73 | HTTPS FTP |
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-Related structure data
Related structure data | 7y4xC 7y54C 7y5jC 7y5rC 7y6eC 7y6oC 7y8hC 7y8iC 7y8sC 7y95C 7y9aC 6zr7S S: Starting model for refinement C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10981.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chelicerata (chelicerates) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-GOL / | #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: 1.97 Å3/Da / Density % sol: 37.67 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2, 0.1 M TRIS pH8.5, 20%(w/v) PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. obs: 39096 / % possible obs: 98.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 12.48 Å2 / CC1/2: 0.98 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.32→1.36 Å / Num. unique obs: 2249 / CC1/2: 0.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZR7 Resolution: 1.32→39.03 Å / SU ML: 0.1658 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.8885 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: 19.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→39.03 Å
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Refine LS restraints |
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LS refinement shell |
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