+Open data
-Basic information
Entry | Database: PDB / ID: 3zx3 | ||||||
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Title | Crystal Structure and Domain Rotation of NTPDase1 CD39 | ||||||
Components | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1 | ||||||
Keywords | HYDROLASE / DOMAIN ROTATION / PURINERGIC SIGNALING | ||||||
Function / homology | Function and homology information 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 / nucleoside diphosphate phosphatase activity / UDP 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 / nucleoside diphosphate phosphatase activity / UDP phosphatase activity / IDP phosphatase activity / cellular response to aluminum ion / GDP phosphatase activity / CTPase activity / ADP phosphatase activity / ADP catabolic process / cellular response to interferon-alpha / negative regulation of dopamine secretion / response to L-arginine / 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 aggregation / platelet activation / synaptic vesicle / cellular response to tumor necrosis factor / basolateral plasma membrane / cellular response to lipopolysaccharide / 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 | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Zebisch, M. / Schaefer, P. / Straeter, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zx3.cif.gz | 658.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zx3.ent.gz | 544.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/3zx3 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zx3 | HTTPS FTP |
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-Related structure data
Related structure data | 3zx0C 3zx2C 3cj1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P97687, apyrase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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