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- PDB-1v8t: Crystal Structure analysis of the ADP-ribose pyrophosphatase comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v8t | ||||||
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Title | Crystal Structure analysis of the ADP-ribose pyrophosphatase complexed with ribose-5'-phosphate and Zn | ||||||
![]() | ADP-ribose pyrophosphatase | ||||||
![]() | HYDROLASE / Nudix motif / MutT family / loop-helix-loop / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / UDP-sugar diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yoshiba, S. / Ooga, T. / Nakagawa, N. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal Authors: Yoshiba, S. / Ooga, T. / Nakagawa, N. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. / Masui, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.8 KB | Display | ![]() |
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PDB format | ![]() | 30.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1v8iC ![]() 1v8lC ![]() 1v8mC ![]() 1v8nC ![]() 1v8rC ![]() 1v8sC ![]() 1v8uC ![]() 1v8vC ![]() 1v8wC ![]() 1v8yC C: citing same article ( |
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Similar structure data | |
Other databases |
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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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Details | dimer,the second part of the biological assembly is generated by y, x, 1-z. |
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Components
#1: Protein | Mass: 19287.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Sugar | ChemComp-R5P / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 5224 / % possible obs: 93.4 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 17 Å2 / Rsym value: 0.04 |
Reflection shell | Resolution: 2.6→2.69 Å / Rsym value: 0.057 / % possible all: 85.6 |
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Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.0609 Å2 / ksol: 0.398819 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→39.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
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Xplor file |
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