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Yorodumi- PDB-6dy1: Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) with fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dy1 | ||||||
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Title | Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) with fatty acid (myristate), in presence of Triton X-100 | ||||||
Components | (N-acylethanolamine acid amidase ...) x 2 | ||||||
Keywords | HYDROLASE / endocannabinoid / lipase | ||||||
Function / homology | Function and homology information N-(long-chain-acyl)ethanolamine deacylase / N-(long-chain-acyl)ethanolamine deacylase activity / N-acylethanolamine metabolic process / sphingosine metabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process ...N-(long-chain-acyl)ethanolamine deacylase / N-(long-chain-acyl)ethanolamine deacylase activity / N-acylethanolamine metabolic process / sphingosine metabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process / fatty acid metabolic process / lysosome / membrane Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å | ||||||
Authors | Gorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Molecular mechanism of activation of the immunoregulatory amidase NAAA. Authors: Gorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dy1.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dy1.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 6dy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/6dy1 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/6dy1 | HTTPS FTP |
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-Related structure data
Related structure data | 6dxwC 6dxxC 6dxyC 6dxzC 6dy0C 6dy2C 6dy3C 5u7zS 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
-N-acylethanolamine acid amidase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 12124.106 Da / Num. of mol.: 1 / Fragment: residues 3-98 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: G1T7U7, N-(long-chain-acyl)ethanolamine deacylase |
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#2: Protein | Mass: 26256.689 Da / Num. of mol.: 1 / Fragment: CBAH domain residues 99-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: G1T7U7, N-(long-chain-acyl)ethanolamine deacylase |
-Sugars , 1 types, 3 molecules
#3: Sugar |
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-Non-polymers , 5 types, 109 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | ChemComp-MYR / | #8: 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: 4.39 Å3/Da / Density % sol: 72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 1.1 M (NH4)2SO4 with 0.1 M sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.998→50 Å / Num. obs: 14498 / % possible obs: 100 % / Redundancy: 73.2 % / Net I/σ(I): 43 |
Reflection shell | Resolution: 2.998→3.11 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U7Z Resolution: 2.998→46.001 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.998→46.001 Å
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Refine LS restraints |
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LS refinement shell |
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