+Open data
-Basic information
Entry | Database: PDB / ID: 6ns1 | |||||||||
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Title | Crystal structure of DIP-gamma IG1+IG2 | |||||||||
Components | Dpr-interacting protein gamma | |||||||||
Keywords | CELL ADHESION / Immunoglobulin superfamily / Glycoprotein / Neuronal / Cell surface receptor | |||||||||
Function / homology | Function and homology information regulation of neuromuscular junction development / Role of ABL in ROBO-SLIT signaling / Signaling by ROBO receptors / : / Regulation of expression of SLITs and ROBOs / neuron projection membrane / photoreceptor cell axon guidance / establishment of synaptic specificity at neuromuscular junction / synapse organization / neuron projection / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Cheng, S. / Park, Y.J. / Kurleto, J.D. / Ozkan, E. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2019 Title: Molecular basis of synaptic specificity by immunoglobulin superfamily receptors in Drosophila. Authors: Cheng, S. / Ashley, J. / Kurleto, J.D. / Lobb-Rabe, M. / Park, Y.J. / Carrillo, R.A. / Ozkan, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ns1.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ns1.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 6ns1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/6ns1 ftp://data.pdbj.org/pub/pdb/validation_reports/ns/6ns1 | HTTPS FTP |
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-Related structure data
Related structure data | 6nrqC 6nrrC 6nrwC 6nrxC 5eo9S S: Starting model for refinement C: citing same article (ref.) |
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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: 24006.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: DIP-gamma, 14521, anon-WO0140519.196, CT34248, Dmel\CG14521, CG14521, Dmel_CG14521 Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VAR6 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#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: 2.29 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.15 M ammonium sulfate, 0.1 M MES, pH 5.5, 25% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2015 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 18742 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.32 % / Biso Wilson estimate: 26.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.158 / Net I/σ(I): 8.81 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1366 / CC1/2: 0.828 / Rrim(I) all: 0.833 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EO9 Resolution: 1.85→43.069 Å / SU ML: 0.21 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / Phase error: 26.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→43.069 Å
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Refine LS restraints |
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LS refinement shell |
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