+Open data
-Basic information
Entry | Database: PDB / ID: 6qgo | ||||||
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Title | Crystal structure of APT1 S119A mutant bound to palmitic acid. | ||||||
Components | Acyl-protein thioesterase 1 | ||||||
Keywords | HYDROLASE / acyl-protein thioesterase / palmitic acid / Depalmitoylation | ||||||
Function / homology | Function and homology information protein depalmitoylation / palmitoyl[protein] hydrolase / negative regulation of Golgi to plasma membrane protein transport / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / phospholipase activity / lipase activity / lysophospholipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity ...protein depalmitoylation / palmitoyl[protein] hydrolase / negative regulation of Golgi to plasma membrane protein transport / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / phospholipase activity / lipase activity / lysophospholipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / eNOS activation / fatty acid transport / fatty acid metabolic process / RAS processing / nuclear membrane / endoplasmic reticulum / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å | ||||||
Authors | Audagnotto, M. / Marcaida, M.J. / Ho, S. / Pojer, F. / Van der Goot, G. / Dal Peraro, M. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains. Authors: Abrami, L. / Audagnotto, M. / Ho, S. / Marcaida, M.J. / Mesquita, F.S. / Anwar, M.U. / Sandoz, P.A. / Fonti, G. / Pojer, F. / Dal Peraro, M. / van der Goot, F.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qgo.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qgo.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qgo_validation.pdf.gz | 624.5 KB | Display | wwPDB validaton report |
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Full document | 6qgo_full_validation.pdf.gz | 628 KB | Display | |
Data in XML | 6qgo_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 6qgo_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/6qgo ftp://data.pdbj.org/pub/pdb/validation_reports/qg/6qgo | HTTPS FTP |
-Related structure data
Related structure data | 6qgnC 6qgqC 6qgsC 1fj2S C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 24977.869 Da / Num. of mol.: 2 / Mutation: S119A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLA1, APT1, LPL1 / Production host: Escherichia coli (E. coli) References: UniProt: O75608, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | ChemComp-PLM / | #3: Water | ChemComp-HOH / | |
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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: 2.77 Å3/Da / Density % sol: 55.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 25% of of polyethylene glycol (PEG) 2000, 0.3 M sodium acetate, 0.1 M sodium cacodylate pH 6.5; |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→48.94 Å / Num. obs: 16831 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.59→2.74 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2432 / CC1/2: 0.78 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FJ2 Resolution: 2.599→48.94 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.599→48.94 Å
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Refine LS restraints |
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LS refinement shell |
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