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- PDB-5ege: Structure of ENPP6, a choline-specific glycerophosphodiester-phos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ege | |||||||||
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Title | Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase | |||||||||
![]() | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 | |||||||||
![]() | HYDROLASE / Choline metabolism / Phosphodiesterase | |||||||||
Function / homology | ![]() glycerophosphocholine cholinephosphodiesterase / glycerophosphocholine cholinephosphodiesterase activity / Glycerophospholipid catabolism / glycerophosphodiester phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / choline metabolic process / lipid catabolic process / lipid metabolic process / extracellular region ...glycerophosphocholine cholinephosphodiesterase / glycerophosphocholine cholinephosphodiesterase activity / Glycerophospholipid catabolism / glycerophosphodiester phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / choline metabolic process / lipid catabolic process / lipid metabolic process / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Morita, J. / Kano, K. / Kato, K. / Takita, H. / Ishitani, R. / Nishimasu, H. / Nureki, O. / Aoki, J. | |||||||||
![]() | ![]() Title: Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase Authors: Morita, J. / Kano, K. / Kato, K. / Takita, H. / Sakagami, H. / Yamamoto, Y. / Mihara, E. / Ueda, H. / Sato, T. / Tokuyama, H. / Arai, H. / Asou, H. / Takagi, J. / Ishitani, R. / Nishimasu, H. ...Authors: Morita, J. / Kano, K. / Kato, K. / Takita, H. / Sakagami, H. / Yamamoto, Y. / Mihara, E. / Ueda, H. / Sato, T. / Tokuyama, H. / Arai, H. / Asou, H. / Takagi, J. / Ishitani, R. / Nishimasu, H. / Nureki, O. / Aoki, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 383.9 KB | Display | ![]() |
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PDB format | ![]() | 310.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49598.664 Da / Num. of mol.: 4 / Fragment: UNP residues 1-421 / Mutation: C393A, C412S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8BGN3, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, glycerophosphocholine cholinephosphodiesterase |
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-Sugars , 3 types, 15 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose 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 #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 2062 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 / Details: ammonium chloride, sodium acetate pH, PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 120105 / % possible obs: 97 % / Redundancy: 4 % / Net I/σ(I): 6.11 |
Reflection shell | Rejects: 0 |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.01 Å2 / Biso mean: 22.2974 Å2 / Biso min: 7.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→41.896 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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