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Open data
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Basic information
Entry | Database: PDB / ID: 4wbh | ||||||
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Title | STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I APO - 2.2A | ||||||
![]() | Protein notum homolog | ||||||
![]() | HYDROLASE / Wnt / extracellular Esterase / alpha/beta hydrolase | ||||||
Function / homology | ![]() [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / bone development / negative regulation of canonical Wnt signaling pathway ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / bone development / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zebisch, M. / Jones, E.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Notum deacylates Wnt proteins to suppress signalling activity Authors: Kakugawa, S. / Langton, P.F. / Zebisch, M. / Howell, S.A. / Chang, T.-H. / Liu, Y. / Feizi, T. / Bineva, G. / O'Reilly, N. / Snijders, A.P. / Jones, E.Y. / Vincent, J.-P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 287.6 KB | Display | ![]() |
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PDB format | ![]() | 236.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.1 KB | Display | ![]() |
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Full document | ![]() | 476.6 KB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uyuC ![]() 4uywC ![]() 4uyzC ![]() 4uz1C ![]() 4uz5C ![]() 4uz6C ![]() 4uz7C ![]() 4uz9C ![]() 4uzaC ![]() 4uzjC ![]() 4uzkC ![]() 4uzlC ![]() 4uzqC 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: 53098.891 Da / Num. of mol.: 2 / Fragment: UNP residues 38-496 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-CL / #3: Sugar | ChemComp-NAG / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 30% PEG3350, 100mM BisTris 6.0, 5% Glycerol, 200mM Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→67 Å / Num. obs: 40214 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4790 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.707 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→87.72 Å
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Refine LS restraints |
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