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Yorodumi- PDB-4uza: STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VIII - PHOSPH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uza | ||||||
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Title | STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VIII - PHOSPHATE COMPLEX - 2.4A | ||||||
Components | PROTEIN NOTUM HOMOLOG | ||||||
Keywords | HYDROLASE / WNT / ESTERASE / EXTRACELLULAR / ALPHA/BETA HYDROLASE | ||||||
Function / homology | Function and homology information [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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å | ||||||
Authors | Zebisch, M. / Jones, E.Y. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Notum Deacylates Wnt Proteins to Suppress Signalling Activity. Authors: Kakugawa, S. / Langton, P.F. / Zebisch, M. / Howell, S.A. / Chang, T. / Liu, Y. / Feizi, T. / Bineva, G. / O'Reilly, N. / Snijders, A.P. / Jones, E.Y. / Vincent, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uza.cif.gz | 153.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uza.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 4uza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uza_validation.pdf.gz | 459.8 KB | Display | wwPDB validaton report |
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Full document | 4uza_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 4uza_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 4uza_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/4uza ftp://data.pdbj.org/pub/pdb/validation_reports/uz/4uza | HTTPS FTP |
-Related structure data
Related structure data | 4uyuC 4uywC 4uyzC 4uz1C 4uz5C 4uz6C 4uz7C 4uz9C 4uzjC 4uzkC 4uzlC 4uzqC 4wbhC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 43426.918 Da / Num. of mol.: 1 / Fragment: RESIDUES 80-452 / Mutation: YES Source method: isolated from a genetically manipulated source Details: GLYCOSYLATED AT N96 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6P988, carboxylesterase |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | pH: 6.3 / Details: 0.630 M K2HPO4 1.170 M NAH2PO4 6.300 PH FINAL PH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: May 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→70 Å / Num. obs: 21598 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.2 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 25 |
-Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.4→134.15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 20.279 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 63.956 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→134.15 Å
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