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Open data
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Basic information
Entry | Database: PDB / ID: 7b9i | ||||||
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Title | Notum Fragment 297 | ||||||
![]() | Palmitoleoyl-protein carboxylesterase NOTUM | ||||||
![]() | HYDROLASE / Notum Inhibitor | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Zhao, Y. / Jones, E.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Analysis and Development of Notum Fragment Screening Hits. Authors: Zhao, Y. / Mahy, W. / Willis, N.J. / Woodward, H.L. / Steadman, D. / Bayle, E.D. / Atkinson, B.N. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Harlos, K. / Jeganathan, F. / Constantinou, S. / ...Authors: Zhao, Y. / Mahy, W. / Willis, N.J. / Woodward, H.L. / Steadman, D. / Bayle, E.D. / Atkinson, B.N. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Harlos, K. / Jeganathan, F. / Constantinou, S. / Costa, A. / Kjaer, S. / Bictash, M. / Salinas, P.C. / Whiting, P. / Vincent, J.P. / Fish, P.V. / Jones, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.9 KB | Display | ![]() |
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PDB format | ![]() | 127 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7b4xC ![]() 7b84C ![]() 7b86C ![]() 7b87C ![]() 7b89C ![]() 7b8cC ![]() 7b8dC ![]() 7b8fC ![]() 7b8gC ![]() 7b8jC ![]() 7b8kC ![]() 7b8lC ![]() 7b8mC ![]() 7b8nC ![]() 7b8oC ![]() 7b8uC ![]() 7b8xC ![]() 7b8yC ![]() 7b8zC ![]() 7b98C ![]() 7b99C ![]() 7b9dC ![]() 7b9nC ![]() 7b9uC ![]() 7ba1C ![]() 7bacC ![]() 7bapC ![]() 7bc8C ![]() 7bc9C ![]() 7bccC ![]() 7bcdC ![]() 7bcfC ![]() 7bchC ![]() 7bciC ![]() 7bckC ![]() 7bclC ![]() 7bd2C ![]() 7bd3C ![]() 7bd4C ![]() 7bd5C ![]() 7bd6C ![]() 7bd8C ![]() 7bd9C ![]() 7bdaC ![]() 7bdbC ![]() 7bdcC ![]() 7bddC ![]() 7bdfC ![]() 7bdgC ![]() 7bdhC ![]() 4uzqS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 43567.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 138 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/T3T.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/T3T.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.42 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate, pH4.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→72.5 Å / Num. obs: 75515 / % possible obs: 95.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.34→1.36 Å / Num. unique obs: 3511 / CC1/2: 0.505 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UZQ Resolution: 1.34→53.4 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.08 / Stereochemistry target values: ML
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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 max: 64.13 Å2 / Biso mean: 21.8374 Å2 / Biso min: 10.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.34→53.4 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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Refinement TLS params. | Method: refined / Origin x: 4.5207 Å / Origin y: -1.1057 Å / Origin z: -1.8389 Å
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Refinement TLS group |
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