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Yorodumi- PDB-1v8l: Structure Analysis of the ADP-ribose pyrophosphatase complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v8l | ||||||
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Title | Structure Analysis of the ADP-ribose pyrophosphatase complexed with ADP-ribose | ||||||
Components | ADP-ribose pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix motif / loop-helix-loop / MutT family / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / UDP-sugar diphosphatase activity / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 1v8l.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v8l.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 1v8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v8l_validation.pdf.gz | 769.9 KB | Display | wwPDB validaton report |
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Full document | 1v8l_full_validation.pdf.gz | 773.7 KB | Display | |
Data in XML | 1v8l_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1v8l_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/1v8l ftp://data.pdbj.org/pub/pdb/validation_reports/v8/1v8l | HTTPS FTP |
-Related structure data
Related structure data | 1v8iC 1v8mC 1v8nC 1v8rC 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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-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) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84CU3, ADP-ribose diphosphatase |
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#2: Chemical | ChemComp-APR / |
#3: 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: 2.28 Å3/Da / Density % sol: 45.53 % |
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-Data collection
Diffraction source | Wavelength: 1.54 Å |
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Detector | Type: RIGAKU RAXIS IV / 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: 2.01→20 Å / Num. obs: 11986 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Biso Wilson estimate: 8.7 Å2 / Rsym value: 0.04 |
Reflection shell | Resolution: 2.01→2.12 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→16.14 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1562121.94 / 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: 56.1279 Å2 / ksol: 0.451683 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→16.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.14 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file |
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