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Open data
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Basic information
Entry | Database: PDB / ID: 8w6p | ||||||
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Title | Crystal structure of dimeric murine SMPDL3A | ||||||
![]() | Acid sphingomyelinase-like phosphodiesterase 3a | ||||||
![]() | HYDROLASE / innate immunity / lipid metabolism | ||||||
Function / homology | ![]() nucleoside triphosphate catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / nucleoside-triphosphate phosphatase / ATP hydrolysis activity / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, C. / Liu, P. / Fan, S. / Hou, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.4 KB | Display | ![]() |
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PDB format | ![]() | 158.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8w6rC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46664.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P70158, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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-Sugars , 5 types, 11 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/FUC.gif)
![](data/chem/img/FUC.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #6: Sugar | ChemComp-NAG / #8: Sugar | ChemComp-FUC / | |
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-Non-polymers , 4 types, 810 molecules ![](data/chem/img/YA4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-YA4 / [( | ||||
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#7: Chemical | ChemComp-ZN / #9: Chemical | ChemComp-PO4 / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion 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: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 16, 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: 1.91→20.27 Å / Num. obs: 89995 / % possible obs: 98.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.91→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1 / Num. unique obs: 3909 / CC1/2: 0.597 / % possible all: 85.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.91→20.27 Å
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Refine LS restraints |
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LS refinement shell |
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