+
Open data
-
Basic information
Entry | Database: PDB / ID: 7dg9 | ||||||
---|---|---|---|---|---|---|---|
Title | DPBB domain of VCP-like ATPase from Aeropyrum pernix | ||||||
![]() | Cell division control protein 48, AAA family | ||||||
![]() | CHAPERONE / Double psi beta barrel | ||||||
Function / homology | ![]() hydrolase activity / cell division / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yagi, S. / Tagami, S. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase. Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S. #1: ![]() Title: Seven amino acid types suffice to reconstruct the core fold of RNA polymerase Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 35.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 22.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 417.9 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dboC ![]() 7dg7C ![]() 7di0C ![]() 7di1C ![]() 7du6C ![]() 7du7C ![]() 7dvcC ![]() 7dvfC ![]() 7dvhC ![]() 7dwwC ![]() 7dxrC ![]() 7dxsC ![]() 7dxtC ![]() 7dxuC ![]() 7dxvC ![]() 7dxwC ![]() 7dxxC ![]() 7dxyC ![]() 7dxzC ![]() 7dycC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10095.523 Da / Num. of mol.: 1 / Fragment: DPBB domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: APE_1367 / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100mM Sodium acetate pH4.5, 20% PEG 1000, 200mM Zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Oct 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 19200 / % possible obs: 98.8 % / Redundancy: 7.21 % / CC1/2: 0.999 / Net I/σ(I): 33.41 |
Reflection shell | Resolution: 1.6→1.7 Å / Num. unique obs: 1569 / CC1/2: 0.979 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.08 Å2 / Biso mean: 14.9658 Å2 / Biso min: 4.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.602→47.078 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|