+Open data
-Basic information
Entry | Database: PDB / ID: 6tuz | |||||||||
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Title | Theophylline-Notum complex | |||||||||
Components | Palmitoleoyl-protein carboxylesterase NOTUM | |||||||||
Keywords | SIGNALING PROTEIN / Wnt Notum inhibitor complex | |||||||||
Function / homology | Function and homology information [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | |||||||||
Authors | Zhao, Y. / Jones, E.Y. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Commun Biol / Year: 2020 Title: Caffeine inhibits Notum activity by binding at the catalytic pocket. Authors: Zhao, Y. / Ren, J. / Hillier, J. / Lu, W. / Jones, E.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tuz.cif.gz | 170.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tuz.ent.gz | 132.8 KB | Display | PDB format |
PDBx/mmJSON format | 6tuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/6tuz ftp://data.pdbj.org/pub/pdb/validation_reports/tu/6tuz | HTTPS FTP |
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-Related structure data
Related structure data | 6tv4C 6r8pS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 43567.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NOTUM, OK/SW-CL.30 / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 207 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-TEP / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.51 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 4.2 / 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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→78.88 Å / Num. obs: 1189310 / % possible obs: 99.6 % / Redundancy: 11.4 % / Biso Wilson estimate: 11.84 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.24→1.26 Å / Num. unique obs: 4742 / CC1/2: 0.541 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R8P Resolution: 1.24→53.633 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.34 Å2 / Biso mean: 21.2903 Å2 / Biso min: 8.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.24→53.633 Å
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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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