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Open data
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Basic information
Entry | Database: PDB / ID: 7alt | ||||||||||||
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Title | Structure of Drosophila Serrate C2-DSL-EGF1-EGF2 | ||||||||||||
![]() | Protein serrate | ||||||||||||
![]() | SIGNALING PROTEIN / Serrate Notch Ligand C2 / DSL and EGF domains | ||||||||||||
Function / homology | ![]() larval salivary gland morphogenesis / eye-antennal disc development / crystal cell differentiation / negative regulation of lamellocyte differentiation / cuticle pattern formation / lateral inhibition / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis / imaginal disc-derived leg segmentation / imaginal disc-derived leg morphogenesis ...larval salivary gland morphogenesis / eye-antennal disc development / crystal cell differentiation / negative regulation of lamellocyte differentiation / cuticle pattern formation / lateral inhibition / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis / imaginal disc-derived leg segmentation / imaginal disc-derived leg morphogenesis / wing disc anterior/posterior pattern formation / larval lymph gland hemopoiesis / compound eye development / imaginal disc-derived wing morphogenesis / glycosphingolipid binding / sensory organ development / germ-line stem cell population maintenance / apical cortex / Notch binding / axolemma / glial cell proliferation / salivary gland morphogenesis / Notch signaling pathway / membrane => GO:0016020 / receptor ligand activity / apical plasma membrane / calcium ion binding / cell surface / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Suckling, R. / Johnson, S. / Lea, S.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The conserved C2 phospholipid-binding domain in Delta contributes to robust Notch signalling. Authors: Martins, T. / Meng, Y. / Korona, B. / Suckling, R. / Johnson, S. / Handford, P.A. / Lea, S.M. / Bray, S.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.4 KB | Display | ![]() |
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PDB format | ![]() | 163.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 824.9 KB | Display | ![]() |
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Full document | ![]() | 830.3 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7aljC ![]() 7alkC ![]() 5mw7S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.999906210829, -0.000599648350543, 0.0136824693301), (-0.000858325876441, 0.999820864457, -0.0189077304919), (-0.0136686803242, -0.0189177011691, -0.999727606781) ...NCS oper: (Code: given Matrix: (-0.999906210829, -0.000599648350543, 0.0136824693301), Vector: |
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Components
#1: Protein | Mass: 29610.537 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | 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: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1M imidazole malate pH 7, 25% PEG4K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→45.61 Å / Num. obs: 38729 / % possible obs: 98.89 % / Redundancy: 3.3 % / Biso Wilson estimate: 31.49 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.03→2.103 Å / Num. unique obs: 3814 / CC1/2: 0.769 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MW7 Resolution: 2.03→45.61 Å / SU ML: 0.2152 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3516 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: 41.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→45.61 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 2.92239358248 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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