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Yorodumi- PDB-1v8r: Crystal structure analysis of the ADP-ribose pyrophosphatase comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v8r | ||||||
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Title | Crystal structure analysis of the ADP-ribose pyrophosphatase complexed with ADP-ribose and Zn | ||||||
Components | ADP-ribose pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix motif / MutT family / loop-helix-loop / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yoshiba, S. / Ooga, T. / Nakagawa, N. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. / Masui, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v8r.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v8r.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 1v8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/1v8r ftp://data.pdbj.org/pub/pdb/validation_reports/v8/1v8r | HTTPS FTP |
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-Related structure data
Related structure data | 1v8iC 1v8lC 1v8mC 1v8nC 1v8sC 1v8tC 1v8uC 1v8vC 1v8wC 1v8yC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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. |
-Components
#1: Protein | Mass: 19287.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q84CU3, ADP-ribose diphosphatase | ||||
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#2: Chemical | #3: Chemical | ChemComp-APR / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.92 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1.282 Å |
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Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 16237 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14 Å2 / Rsym value: 0.052 |
Reflection shell | Resolution: 1.8→1.86 Å / Rsym value: 0.096 / % possible all: 99.6 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.02 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 921685.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 76.0493 Å2 / ksol: 0.506776 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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