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- PDB-3cj9: Structure of Rattus norvegicus NTPDase2 in complex with calcium, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cj9 | ||||||
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Title | Structure of Rattus norvegicus NTPDase2 in complex with calcium, AMP and phosphate | ||||||
![]() | Ectonucleoside triphosphate diphosphohydrolase 2 | ||||||
![]() | HYDROLASE / alpha/beta protein / Actin-like fold / Alternative splicing / Calcium / Glycoprotein / Magnesium / Membrane / Transmembrane | ||||||
Function / homology | ![]() purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / UDP phosphatase activity / nucleoside diphosphate phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane ...purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / UDP phosphatase activity / nucleoside diphosphate phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane / cellular response to interleukin-6 / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / basement membrane / ribonucleoside triphosphate phosphatase activity / platelet activation / cellular response to tumor necrosis factor / cell body / cellular response to lipopolysaccharide / G protein-coupled receptor signaling pathway / cell surface / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zebisch, M. / Strater, N. | ||||||
![]() | ![]() Title: Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling Authors: Zebisch, M. / Strater, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 101.7 KB | Display | ![]() |
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PDB format | ![]() | 81.1 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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Unit cell |
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Components
#1: Protein | Mass: 50611.949 Da / Num. of mol.: 1 Fragment: Ectodomain, Extracellular domain, UNP residues 29-461 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-AMP / |
#5: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ENTP2_RAT. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 100mM NaHEPES, 2% PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25.47 Å / Num. obs: 44443 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Redundancy: 7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.333 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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