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- PDB-4br7: Legionella pneumophila NTPDase1 crystal form I, open, AMPNP complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 4br7 | ||||||
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Title | Legionella pneumophila NTPDase1 crystal form I, open, AMPNP complex | ||||||
![]() | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I | ||||||
![]() | HYDROLASE / APYRASE / ATPASE / ADPASE / CD39 / PURINERGIC SIGNALLING / DOMAIN ROTATION / TRANSITION STATE / NTPDASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zebisch, M. / Schaefer, P. / Lauble, P. / Straeter, N. | ||||||
![]() | ![]() Title: Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases Authors: Zebisch, M. / Krauss, M. / Schaefer, P. / Lauble, P. / Straeter, 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 | ![]() | 159.5 KB | Display | ![]() |
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PDB format | ![]() | 132.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772 KB | Display | ![]() |
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Full document | ![]() | 775.6 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bqzC ![]() 4br0C ![]() 4br2C ![]() 4br4C ![]() 4br5C ![]() 4br9C ![]() 4braC ![]() 4brcC ![]() 4brdC ![]() 4breC ![]() 4brfC ![]() 4brgC ![]() 4brhC ![]() 4briC ![]() 4brkC ![]() 4brlC ![]() 4brmC ![]() 4brnC ![]() 4broC ![]() 4brpC ![]() 4brqC C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 41537.230 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | ChemComp-AU1 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | PHOSPHOAMI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 7.7 Details: 30% PEP 629 (PENTAERYTHRITOL PROPOXYLATE 17/8 PO/OH), 100MM NAHEPES PH 7.7, 50MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9181 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29 Å / Num. obs: 42613 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6 |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.8→27.61 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.519 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.106 / 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: 27.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.61 Å
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Refine LS restraints |
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