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Yorodumi- PDB-4x9i: Crystal structure of Dscam1 isoform 9.44, N-terminal four Ig domains -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x9i | |||||||||
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Title | Crystal structure of Dscam1 isoform 9.44, N-terminal four Ig domains | |||||||||
Components | Down Syndrome Cell Adhesion Molecule, isoform 9.44 | |||||||||
Keywords | CELL ADHESION / Ig fold | |||||||||
Function / homology | Function and homology information mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / dendrite self-avoidance / cell-cell adhesion mediator activity / axon extension involved in axon guidance / axon guidance receptor activity / peripheral nervous system development ...mushroom body development / detection of mechanical stimulus involved in sensory perception of touch / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / dendrite self-avoidance / cell-cell adhesion mediator activity / axon extension involved in axon guidance / axon guidance receptor activity / peripheral nervous system development / axonal fasciculation / regulation of dendrite morphogenesis / regulation of axonogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / neuron development / phagocytosis / antigen binding / axon guidance / neuron projection / axon / neuronal cell body / dendrite / protein homodimerization activity / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.904 Å | |||||||||
Authors | Chen, Q. / Yu, Y. / Li, S.A. / cheng, L. | |||||||||
Citation | Journal: Sci Adv / Year: 2016 Title: Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition Authors: Li, S.A. / Cheng, L. / Yu, Y. / Chen, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x9i.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x9i.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 4x9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/4x9i ftp://data.pdbj.org/pub/pdb/validation_reports/x9/4x9i | HTTPS FTP |
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-Related structure data
Related structure data | 4wvrC 4x5lC 4x83C 4x8xC 4x9bC 4x9fC 4x9gC 4x9hC 4xb7C 4xb8C 4xhqC 2v5mS 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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Unit cell |
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-Components
#1: Protein | Mass: 43414.879 Da / Num. of mol.: 2 / Fragment: N-terminal four Ig domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0E9L5*PLUS #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M Sodium acetate, pH 4.6, 25% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 20863 / % possible obs: 96.6 % / Redundancy: 3 % / Net I/σ(I): 8.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V5M Resolution: 2.904→45.49 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.52 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.904→45.49 Å
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Refine LS restraints |
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LS refinement shell |
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