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Yorodumi- PDB-4uz6: STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM V - SOS COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uz6 | |||||||||
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Title | STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM V - SOS COMPLEX - 1.9A | |||||||||
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: 1.9 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 | 4uz6.cif.gz | 296.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uz6.ent.gz | 244.6 KB | Display | PDB format |
PDBx/mmJSON format | 4uz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/4uz6 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/4uz6 | HTTPS FTP |
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-Related structure data
Related structure data | 4uyuC 4uywC 4uyzC 4uz1C 4uz5C 4uz7C 4uz9C 4uzaC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.003, 0.988, -0.152), Vector: |
-Components
#1: Protein | Mass: 43567.148 Da / Num. of mol.: 2 / Fragment: RESIDUES 81-451 / 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 #2: Polysaccharide | #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | C330S ENGINEERED | |
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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 20 %W/V PEG3350, 0.2 M AMMONIUM SULFATE 20MM SOS, pH 7.5 |
-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: 1.9→34.4 Å / Num. obs: 72075 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.7 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.9→97.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.564 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.132 / 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: 38.157 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→97.9 Å
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Refine LS restraints |
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