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- PDB-3x0n: ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESM-s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3x0n | ||||||
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Title | ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESM-state at reaction time of 6 min | ||||||
![]() | ADP-ribose pyrophosphatase | ||||||
![]() | HYDROLASE / Nudix motif / ADP ribose hydrolase / ADP ribose / Cytosol | ||||||
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 / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Furuike, Y. / Akita, Y. / Miyahara, I. / Kamiya, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 65.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3x0iSC ![]() 3x0jC ![]() 3x0kC ![]() 3x0lC ![]() 3x0mC ![]() 3x0oC ![]() 3x0pC ![]() 3x0qC ![]() 3x0rC ![]() 3x0sC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 127 molecules ![](data/chem/img/AR6.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AR6 / [( |
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#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.04 % |
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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, 8%(w/v) PEG 20000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 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: 1.12→30 Å / Num. all: 66244 / Num. obs: 66244 / % 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: ![]() Starting model: 3X0I Resolution: 1.12→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 1.12→30 Å
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Refine LS restraints |
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