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Open data
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Basic information
Entry | Database: PDB / ID: 3zx3 | ||||||
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Title | Crystal Structure and Domain Rotation of NTPDase1 CD39 | ||||||
![]() | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1 | ||||||
![]() | HYDROLASE / DOMAIN ROTATION / PURINERGIC SIGNALING | ||||||
Function / homology | ![]() response to proline / CDP phosphatase activity / ITPase activity / apyrase / apyrase activity / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / UDP phosphatase activity / nucleoside diphosphate phosphatase activity ...response to proline / CDP phosphatase activity / ITPase activity / apyrase / apyrase activity / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / nucleoside diphosphate catabolic process / UDP phosphatase activity / nucleoside diphosphate phosphatase activity / IDP phosphatase activity / cellular response to aluminum ion / ADP phosphatase activity / CTPase activity / GDP phosphatase activity / ADP catabolic process / cellular response to interferon-alpha / response to L-arginine / negative regulation of dopamine secretion / negative regulation of ATP biosynthetic process / response to auditory stimulus / response to caffeine / response to ATP / basement membrane / ribonucleoside triphosphate phosphatase activity / synaptic membrane / caveola / response to gamma radiation / platelet activation / platelet aggregation / synaptic vesicle / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / basolateral plasma membrane / response to lipopolysaccharide / G protein-coupled receptor signaling pathway / external side of plasma membrane / GTPase activity / neuronal cell body / cell surface / ATP hydrolysis activity / extracellular space / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zebisch, M. / Schaefer, P. / Straeter, N. | ||||||
![]() | ![]() Title: Crystallographic Evidence for a Domain Motion in Rat Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) 1. Authors: Zebisch, M. / Krauss, M. / Schafer, P. / 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 | ![]() | 658.4 KB | Display | ![]() |
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PDB format | ![]() | 544.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zx0C ![]() 3zx2C ![]() 3cj1S C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 50576.953 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 38-189,190-206 Source method: isolated from a genetically manipulated source Details: A PUTATIVE MEMBRANE INTERACTION LOOP 190TQEQSWLNFISDSQKQA206 WAS REPLACED BY A SHORTER LINKER KTPGGS Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-ACY / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Sequence details | THE LOOP T190 TO A206 WAS REPLACED WITH THE SEQUENCE KTPGGS OF GB EDL94186.1. THE RESIDUES 80, 220, ...THE LOOP T190 TO A206 WAS REPLACED WITH THE SEQUENCE KTPGGS OF GB EDL94186.1. THE RESIDUES 80, 220, AND 227 MATCH THE GENBANK SEQUENCE. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 4.5 / Details: 3.6 M NACL, 100 MM NAAC PH 4.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→42.55 Å / Num. obs: 151721 / % possible obs: 72.4 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4 / % possible all: 7.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CJ1 Resolution: 1.7→146.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 45.504 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→146.62 Å
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LS refinement shell | Resolution: 1.703→1.747 Å / Total num. of bins used: 20
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