+Open data
-Basic information
Entry | Database: PDB / ID: 4x5l | ||||||
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Title | Crystal structure of Dscam1 Ig7 domain, isoform 9 | ||||||
Components | Down syndrome cell adhesion molecule, isoform AM | ||||||
Keywords | CELL ADHESION / Ig fold | ||||||
Function / homology | Function and homology information detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / detection of mechanical stimulus involved in sensory perception of touch / ventral cord development / dendrite self-avoidance / axon extension involved in axon guidance / axon guidance receptor activity / peripheral nervous system development / axonal fasciculation ...detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / detection of mechanical stimulus involved in sensory perception of touch / ventral cord development / dendrite self-avoidance / axon extension involved in axon guidance / axon guidance receptor activity / peripheral nervous system development / axonal fasciculation / regulation of axonogenesis / regulation of dendrite morphogenesis / plasma membrane => GO:0005886 / neuron development / phagocytosis / antigen binding / axon guidance / cell adhesion / neuron projection / axon / neuronal cell body / dendrite / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.374 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 | 4x5l.cif.gz | 148 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x5l.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 4x5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/4x5l ftp://data.pdbj.org/pub/pdb/validation_reports/x5/4x5l | HTTPS FTP |
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-Related structure data
Related structure data | 4wvrC 4x83C 4x8xC 4x9bC 4x9fC 4x9gC 4x9hC 4x9iC 4xb7C 4xb8C 4xhqC 3dmkS 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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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10737.034 Da / Num. of mol.: 4 / Fragment: UNP residues 617-713 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dscam1, Dscam, CG17800, Dmel_CG17800 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0E9K7 #2: Chemical | #3: 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: 3.65 Å3/Da / Density % sol: 66.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES PH 7.5, 0.7 M sodium phosphate monobasic, 0.7 M potassium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979104 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979104 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→50 Å / Num. obs: 26120 / % possible obs: 99.5 % / Redundancy: 7.1 % / Net I/σ(I): 21.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DMK Resolution: 2.374→45.527 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.86 / Stereochemistry target values: TWIN_LSQ_F
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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: 2.374→45.527 Å
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Refine LS restraints |
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LS refinement shell |
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