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Open data
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Basic information
Entry | Database: PDB / ID: 4cbz | ||||||
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Title | Notch ligand, Jagged-1, contains an N-terminal C2 domain | ||||||
![]() | PROTEIN JAGGED-1 | ||||||
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Function / homology | ![]() endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / Nephron development / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet ...endocardial cushion cell development / loop of Henle development / ciliary body morphogenesis / Nephron development / regulation of reproductive process / pulmonary artery morphogenesis / cardiac neural crest cell development involved in outflow tract morphogenesis / podocyte development / negative regulation of endothelial cell differentiation / morphogenesis of an epithelial sheet / nephron development / positive regulation of myeloid cell differentiation / cardiac right ventricle morphogenesis / inhibition of neuroepithelial cell differentiation / distal tubule development / neuroendocrine cell differentiation / aorta morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / T cell mediated immunity / positive regulation of cardiac epithelial to mesenchymal transition / NOTCH4 Activation and Transmission of Signal to the Nucleus / inner ear auditory receptor cell differentiation / endothelial cell differentiation / neuronal stem cell population maintenance / pulmonary valve morphogenesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chilakuri, C.R. / Sheppard, D. / Ilagan, M.X.G. / Holt, L.R. / Abbott, F. / Liang, S. / Kopan, R. / Handford, P.A. / Lea, S.M. | ||||||
![]() | ![]() Title: Structural Analysis Uncovers Lipid-Binding Properties of Notch Ligands Authors: Chilakuri, C.R. / Sheppard, D. / Ilagan, M.X.G. / Holt, L.R. / Abbott, F. / Liang, S. / Kopan, R. / Handford, P.A. / Lea, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.1 KB | Display | ![]() |
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PDB format | ![]() | 185.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cc0C ![]() 4cc1C ![]() 2vj2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.248, -0.594, 0.766), Vector ![]() |
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Components
#1: Protein | Mass: 34813.750 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-335 Source method: isolated from a genetically manipulated source Details: NAG LINKAGE AT N217 IN BOTH A, B CHAINS, FUC LINKAGE AT T311 IN A CHAIN Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | ![]() #3: Sugar | ChemComp-FUC / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.39 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→61.12 Å / Num. obs: 22857 / % possible obs: 82.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 74.84 Å2 / Rmerge(I) obs: 0.12 |
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Processing
Software | Name: BUSTER / Version: 2.11.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2VJ2 Resolution: 2.5→61.12 Å / Cor.coef. Fo:Fc: 0.9298 / Cor.coef. Fo:Fc free: 0.8996 / SU R Cruickshank DPI: 0.477 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.438 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.283
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Displacement parameters | Biso mean: 70.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.386 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→61.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.62 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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