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Yorodumi- PDB-5u84: Acid ceramidase (ASAH1, aCDase) from common minke whale, Cys143Al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u84 | |||||||||
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Title | Acid ceramidase (ASAH1, aCDase) from common minke whale, Cys143Ala, uncleaved | |||||||||
Components | Acid ceramidase | |||||||||
Keywords | HYDROLASE / ceramidase / ceramide / ntn-hydrolase | |||||||||
Function / homology | Function and homology information ceramidase / N-acylsphingosine amidohydrolase activity / : / fatty acid amide hydrolase activity / sphingolipid metabolic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / fatty acid metabolic process / lysosome / extracellular region Similarity search - Function | |||||||||
Biological species | Balaenoptera acutorostrata (minke whale) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | |||||||||
Authors | Gebai, A. / Gorelik, A. / Illes, K. / Nagar, B. | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for the activation of acid ceramidase. Authors: Gebai, A. / Gorelik, A. / Li, Z. / Illes, K. / Nagar, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u84.cif.gz | 283.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u84.ent.gz | 237.2 KB | Display | PDB format |
PDBx/mmJSON format | 5u84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/5u84 ftp://data.pdbj.org/pub/pdb/validation_reports/u8/5u84 | HTTPS FTP |
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-Related 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43862.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Balaenoptera acutorostrata (minke whale) Gene: ASAH1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A383ZFX3, ceramidase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 177 molecules
#4: Chemical | ChemComp-I3C / #5: Chemical | ChemComp-IOD / #6: 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: 2.87 Å3/Da / Density % sol: 57.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: citric acid sodium chloride lithium 5-amino-2,4,6-triiodoisophthalate (I3C) PH range: 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.77122 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77122 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→44.656 Å / Num. obs: 67018 / % possible obs: 99 % / Redundancy: 6.8 % / Net I/σ(I): 14.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→44.656 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→44.656 Å
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Refine LS restraints |
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LS refinement shell |
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