[English] 日本語
![](img/lk-miru.gif)
- PDB-6f2v: Crystal structure of ectonucleotide phosphodiesterase/pyrophospha... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6f2v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) in complex with AMP | |||||||||
![]() | Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 | |||||||||
![]() | HYDROLASE / enzyme / ectonucleotide phosphodiesterase/pyrophosphatase / complex / CYTOSOLIC PROTEIN | |||||||||
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 | ![]()
| |||||||||
![]() | ![]() Title: Crystal structure and substrate binding mode of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3). Authors: Dohler, C. / Zebisch, M. / Strater, N. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 610.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 500.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 54.3 KB | Display | |
Data in CIF | ![]() | 77 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f2tC ![]() 6f2yC ![]() 6f30C ![]() 6f33C ![]() 2xr9S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
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 |
---|
-Sugars , 3 types, 10 molecules ![](data/chem/img/NAG.gif)
#2: 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 #3: 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 | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 4 types, 472 molecules ![](data/chem/img/AMP.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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.84 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2013 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→37.81 Å / Num. obs: 70943 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 56.69 Å2 / Rpim(I) all: 0.097 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.5→2.54 Å |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2XR9 Resolution: 2.5→37.81 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.917 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.355 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.218
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.37 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.34 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.5→37.81 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|