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Open data
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Basic information
Entry | Database: PDB / ID: 3aap | ||||||
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Title | Crystal Structure of Lp1NTPDase from Legionella pneumophila | ||||||
![]() | Ectonucleoside triphosphate diphosphohydrolase I | ||||||
![]() | HYDROLASE / Adenosine Triphosphatase / NTPDase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vivian, J.P. / Beddoe, T. / Rossjohn, J. | ||||||
![]() | ![]() Title: Crystal Structure of a Legionella pneumophila Ecto -Triphosphate Diphosphohydrolase, A Structural and Functional Homolog of the Eukaryotic NTPDases Authors: Vivian, J.P. / Riedmaier, P. / Ge, H. / Le Nours, J. / Sansom, F.M. / Wilce, M.C.J. / Byres, E. / Dias, M. / Schmidberger, J.W. / Cowan, P.J. / d'Apice, A.J.F. / Hartland, E.L. / Rossjohn, J. / Beddoe, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.5 KB | Display | ![]() |
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PDB format | ![]() | 68.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.1 KB | Display | ![]() |
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Full document | ![]() | 425.6 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aaqC ![]() 3aarC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 40032.625 Da / Num. of mol.: 1 / Fragment: UNP residues 41-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | ACCORDING TO AUTHOR, RESIDUE 149VAL IS A NATURAL VARIANT OF UNIPROT/TREMBL Q5ZUA2, AND WILL BE ...ACCORDING TO AUTHOR, RESIDUE 149VAL IS A NATURAL VARIANT OF UNIPROT/TREMBL Q5ZUA2, AND WILL BE REPORTED TO UNIPROT. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20-24%(w/v) PEG 3350, 0.2M Na Formate, 0.1M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 62027 / % possible obs: 99.9 % / Redundancy: 21.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CJ1 Resolution: 1.6→37.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.376 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 21.226 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→37.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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