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Yorodumi- PDB-3cja: Structure of Rattus norvegicus NTPDase2 in complex with calcium a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cja | ||||||
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Title | Structure of Rattus norvegicus NTPDase2 in complex with calcium and AMPPNP | ||||||
Components | Ectonucleoside triphosphate diphosphohydrolase 2 | ||||||
Keywords | HYDROLASE / alpha/beta protein / Actin-like fold / Alternative splicing / Calcium / Glycoprotein / Magnesium / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / nucleoside diphosphate phosphatase activity / UDP phosphatase activity / GDP phosphatase activity / ADP 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 / nucleoside diphosphate phosphatase activity / UDP phosphatase activity / GDP phosphatase activity / ADP 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 / cell body / cellular response to tumor necrosis factor / 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å | ||||||
Authors | Zebisch, M. / Strater, N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cja.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cja.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 3cja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/3cja ftp://data.pdbj.org/pub/pdb/validation_reports/cj/3cja | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Rattus norvegicus (Norway rat) / Gene: Entpd2 / Plasmid: pET45b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: O35795, apyrase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-ANP / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ENTP2_RAT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46 % |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 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: 2.1→26.67 Å / Num. obs: 26670 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.1→26.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.844 / SU ML: 0.115 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→26.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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