+Open data
-Basic information
Entry | Database: PDB / ID: 8w6r | |||||||||
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Title | murine SMPDL3A bound to sulfate | |||||||||
Components | Acid sphingomyelinase-like phosphodiesterase 3a | |||||||||
Keywords | HYDROLASE / innate immunity / lipid metabolism | |||||||||
Function / homology | Function and homology information nucleoside triphosphate catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / nucleoside-triphosphate phosphatase / extracellular space / zinc ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Zhang, C. / Liu, P. / Fan, S. | |||||||||
Funding support | China, 2items
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Citation | Journal: Immunity / Year: 2023 Title: SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing. Authors: Hou, Y. / Wang, Z. / Liu, P. / Wei, X. / Zhang, Z. / Fan, S. / Zhang, L. / Han, F. / Song, Y. / Chu, L. / Zhang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w6r.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w6r.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 8w6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/8w6r ftp://data.pdbj.org/pub/pdb/validation_reports/w6/8w6r | HTTPS FTP |
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-Related structure data
Related structure data | 8w6pC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47540.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smpdl3a, Asml3a / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P70158, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#3: Sugar |
-Non-polymers , 3 types, 369 molecules
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.13 Å3/Da / Density % sol: 60.75 % |
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Crystal grow | Temperature: 291 K / Method: evaporation Details: 0.1 M sodium citrate [pH 5.5], 0.2M ammonium sulfate and 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20.54 Å / Num. obs: 42004 / % possible obs: 97.7 % / Redundancy: 9.1 % / Biso Wilson estimate: 21.61 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.157 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2041 / CC1/2: 0.733 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20.54 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20.54 Å
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Refine LS restraints |
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LS refinement shell |
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