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Open data
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Basic information
Entry | Database: PDB / ID: 3s86 | ||||||
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Title | Crystal Structure of TM0159 with bound IMP | ||||||
![]() | Nucleoside-triphosphatase![]() | ||||||
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Function / homology | ![]() XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sommerhalter, M. / Smith, C. / Awwad, K. / Desai, A. | ||||||
![]() | ![]() Title: Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima. Authors: Awwad, K. / Desai, A. / Smith, C. / Sommerhalter, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.7 KB | Display | ![]() |
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PDB format | ![]() | 130.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | ![]() Mass: 23834.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9WY06, nucleoside-triphosphate phosphatase #2: Chemical | ChemComp-IMP / ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG3350, L-Proline, Tris-HCl pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→50 Å / Num. all: 48209 / Num. obs: 48090 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.15→2.2 Å / Mean I/σ(I) obs: 3.05 / Num. unique all: 3160 / % possible all: 100 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.39 Å2 / Biso mean: 46.8774 Å2 / Biso min: 22.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→28.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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