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Open data
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Basic information
Entry | Database: PDB / ID: 6ns1 | |||||||||
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Title | Crystal structure of DIP-gamma IG1+IG2 | |||||||||
![]() | Dpr-interacting protein gamma | |||||||||
![]() | CELL ADHESION / Immunoglobulin superfamily / Glycoprotein / Neuronal / Cell surface receptor | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cheng, S. / Park, Y.J. / Kurleto, J.D. / Ozkan, E. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.2 KB | Display | ![]() |
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PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.9 KB | Display | ![]() |
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Full document | ![]() | 757.1 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nrqC ![]() 6nrrC ![]() 6nrwC ![]() 6nrxC ![]() 5eo9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: DIP-gamma, 14521, anon-WO0140519.196, CT34248, Dmel\CG14521, CG14521, Dmel_CG14521 Cell line (production host): High Five cells / Production host: ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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