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Yorodumi- PDB-3x0s: ADP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x0s | ||||||
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Title | ADP ribose pyrophosphatase from Thermus thermophilus HB8 in E'-state at reaction time of 50 min | ||||||
Components | ADP-ribose pyrophosphatase | ||||||
Keywords | HYDROLASE / Nudix motif / ADP ribose hydrolase / ADP ribose / Cytosol | ||||||
Function / homology | Function and homology information 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 / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Furuike, Y. / Akita, Y. / Miyahara, I. / Kamiya, N. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: ADP-Ribose Pyrophosphatase Reaction in Crystalline State Conducted by Consecutive Binding of Two Manganese(II) Ions as Cofactors Authors: Furuike, Y. / Akita, Y. / Miyahara, I. / Kamiya, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x0s.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x0s.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 3x0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x0s_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 3x0s_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 3x0s_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 3x0s_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/3x0s ftp://data.pdbj.org/pub/pdb/validation_reports/x0/3x0s | HTTPS FTP |
-Related structure data
Related structure data | 3x0iSC 3x0jC 3x0kC 3x0lC 3x0mC 3x0nC 3x0oC 3x0pC 3x0qC 3x0rC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 HB8 (bacteria) / Strain: HB8 / Gene: TTHA0528 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKW5, ADP-ribose diphosphatase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MN / | #5: 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: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.24M Acetate-Sodium acetate buffer, 0.32M Ammonium sulfate, 30%(w/v) Glycerol, 6%(w/v) PEG 20000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2012 | ||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Fixed exit Si (111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→30 Å / Num. all: 69805 / Num. obs: 69805 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X0I Resolution: 1.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.1→30 Å
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Refine LS restraints |
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