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Open data
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Basic information
Entry | Database: PDB / ID: 3zx0 | |||||||||
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Title | NTPDase1 in complex with Heptamolybdate | |||||||||
![]() | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1 | |||||||||
![]() | HYDROLASE / DOMAIN ROTATION / POLYOXOMETALLATE / METAL CLUSTER / PURINERGIC SIGNALING | |||||||||
Function / homology | ![]() response to proline / CDP phosphatase activity / apyrase / ITPase activity / apyrase activity / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / IDP phosphatase activity / cellular response to aluminum ion ...response to proline / CDP phosphatase activity / apyrase / ITPase activity / apyrase activity / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / IDP phosphatase activity / cellular response to aluminum ion / ADP phosphatase activity / CTPase activity / GDP phosphatase activity / nucleoside diphosphate catabolic process / ADP catabolic process / cellular response to interferon-alpha / nucleoside diphosphate phosphatase activity / 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 / membrane scission GTPase motor activity / ribonucleoside triphosphate phosphatase activity / response to gamma radiation / synaptic membrane / caveola / 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 / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader 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 | ![]() | 635.1 KB | Display | ![]() |
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PDB format | ![]() | 529 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 58.3 KB | Display | |
Data in CIF | ![]() | 78.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zx2C ![]() 3zx3C ![]() 3cj1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 50592.953 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 38-189,206-477 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-MO7 / #5: Chemical | ChemComp-NA / Has protein modification | Y | 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: 4.2 / Details: 3.8M NACL, 100MM NAACETAT PH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89461 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.15 Å / Num. obs: 57453 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 65.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.5→2.63 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2 / % possible all: 28.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CJ1 Resolution: 2.5→145.73 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 25.855 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.773 / ESU R Free: 0.318 / 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: 72.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→145.73 Å
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Refine LS restraints |
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