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- PDB-6f2t: Crystal structure of ectonucleotide phosphodiesterase/pyrophospha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f2t | |||||||||
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Title | Crystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) | |||||||||
![]() | Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 | |||||||||
![]() | HYDROLASE / enzyme / ectonucleotide phosphodiesterase/pyrophosphatase | |||||||||
Function / homology | ![]() basophil activation involved in immune response / negative regulation of mast cell activation involved in immune response / phosphodiesterase I / dinucleotide phosphatase activity / nucleotide diphosphatase / nucleoside triphosphate catabolic process / regulation of smooth muscle cell differentiation / negative regulation of mast cell proliferation / nucleoside triphosphate diphosphatase activity / pyrimidine nucleotide metabolic process ...basophil activation involved in immune response / negative regulation of mast cell activation involved in immune response / phosphodiesterase I / dinucleotide phosphatase activity / nucleotide diphosphatase / nucleoside triphosphate catabolic process / regulation of smooth muscle cell differentiation / negative regulation of mast cell proliferation / nucleoside triphosphate diphosphatase activity / pyrimidine nucleotide metabolic process / phosphate ion homeostasis / phosphodiesterase I activity / phosphate-containing compound metabolic process / ATP metabolic process / negative regulation of inflammatory response / nucleic acid binding / apical plasma membrane / external side of plasma membrane / calcium ion binding / perinuclear region of cytoplasm / cell surface / zinc ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dohler, C. / Zebisch, M. / Strater, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure and substrate binding mode of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3). Authors: Dohler, C. / Zebisch, M. / Strater, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 599.1 KB | Display | ![]() |
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PDB format | ![]() | 493.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 53.4 KB | Display | |
Data in CIF | ![]() | 76.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f2vC ![]() 6f2yC ![]() 6f30C ![]() 6f33C ![]() 2xr9S S: Starting model for refinement C: citing same article ( |
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Similar 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 85399.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P97675, phosphodiesterase I, nucleotide diphosphatase |
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-Sugars , 3 types, 9 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 482 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-ZN / #6: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.25 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2 M KCl, 0.1 M MgAcetate, 0.05 NaCacodylate pH 6.0, 10.2% PEG8000, 1 mM CaCl2, 0.1 mM ZnSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2015 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91843 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.35 Å / Num. obs: 76975 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 63.1 Å2 / Rpim(I) all: 0.131 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.4→2.45 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XR9 Resolution: 2.4→47.35 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.331 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.219
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Displacement parameters | Biso mean: 57.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→47.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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