+
Open data
-
Basic information
| Entry | Database: PDB / ID: 3zx0 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | NTPDase1 in complex with Heptamolybdate | |||||||||
Components | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 1 | |||||||||
Keywords | HYDROLASE / DOMAIN ROTATION / POLYOXOMETALLATE / METAL CLUSTER / PURINERGIC SIGNALING | |||||||||
| Function / homology | Function and homology informationresponse 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 / CTPase activity / ADP phosphatase activity / GDP phosphatase activity / nucleoside diphosphate catabolic process / ADP catabolic process / nucleoside diphosphate phosphatase activity / negative regulation of dopamine secretion / cellular response to interferon-alpha / response to L-arginine / negative regulation of ATP biosynthetic process / response to auditory stimulus / response to caffeine / response to ATP / basement membrane / synaptic membrane / ribonucleoside triphosphate phosphatase activity / response to gamma radiation / caveola / platelet activation / platelet aggregation / synaptic vesicle / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to lipopolysaccharide / basolateral plasma membrane / G protein-coupled receptor signaling pathway / external side of plasma membrane / neuronal cell body / GTPase activity / cell surface / ATP hydrolysis activity / extracellular space / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Zebisch, M. / Schaefer, P. / Straeter, N. | |||||||||
Citation | Journal: J. Mol. Biol. / Year: 2012Title: Crystallographic evidence for a domain motion in rat nucleoside triphosphate diphosphohydrolase (NTPDase) 1. Authors: Zebisch, M. / Krauss, M. / Schafer, P. / Strater, N. | |||||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 3zx0.cif.gz | 635.1 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb3zx0.ent.gz | 529 KB | Display | PDB format |
| PDBx/mmJSON format | 3zx0.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 3zx0_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 3zx0_full_validation.pdf.gz | 2.4 MB | Display | |
| Data in XML | 3zx0_validation.xml.gz | 58.3 KB | Display | |
| Data in CIF | 3zx0_validation.cif.gz | 78.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/3zx0 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zx0 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 3zx2C ![]() 3zx3C ![]() 3cj1S C: citing same article ( S: Starting model for refinement |
|---|---|
| Similar structure data |
-
Links
-
Assembly
| Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
|
-
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. | |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
|---|---|
| Crystal grow | pH: 4.2 / Details: 3.8M NACL, 100MM NAACETAT PH 4.2 |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.89461 |
| 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 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.5→145.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi





X-RAY DIFFRACTION
Citation












PDBj









