[English] 日本語
![](img/lk-miru.gif)
- PDB-3x0m: ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESM-s... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3x0m | ||||||
---|---|---|---|---|---|---|---|
Title | ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESM-state at reaction time of 3 min | ||||||
![]() | ADP-ribose pyrophosphatase | ||||||
![]() | HYDROLASE / Nudix motif / ADP ribose hydrolase / ADP ribose / Cytosol | ||||||
Function / homology | ![]() 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 / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 90 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 792.6 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3x0iSC ![]() 3x0jC ![]() 3x0kC ![]() 3x0lC ![]() 3x0nC ![]() 3x0oC ![]() 3x0pC ![]() 3x0qC ![]() 3x0rC ![]() 3x0sC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 148 molecules ![](data/chem/img/AR6.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AR6 / [( |
---|---|
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-MN / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: ES100=0.24M Acetate-Sodium acetate buffer, 0.32M Ammonium sulfate, 30%(w/v) Glycerol, 9%(w/v) PEG 20000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→20 Å / Num. all: 60829 / Num. obs: 60829 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3X0I Resolution: 1.15→20 Å / Stereochemistry target values: Engh & Huber /
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→20 Å
| ||||||||||||
Refine LS restraints |
|