[English] 日本語
![](img/lk-miru.gif)
- PDB-7dvf: Crystal structure of the computationally designed reDPBB_sym2 protein -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7dvf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the computationally designed reDPBB_sym2 protein | ||||||
![]() | reDPBB_sym2 protein | ||||||
![]() | CHAPERONE / Double psi beta barrel | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yagi, S. / Tagami, S. / Padhi, A.K. / Zhang, K.Y.J. | ||||||
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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 52.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dboC ![]() 7dg7C ![]() 7dg9C ![]() 7di0C ![]() 7di1C ![]() 7du6SC ![]() 7du7C ![]() 7dvcC ![]() 7dvhC ![]() 7dwwC ![]() 7dxrC ![]() 7dxsC ![]() 7dxtC ![]() 7dxuC ![]() 7dxvC ![]() 7dxwC ![]() 7dxxC ![]() 7dxyC ![]() 7dxzC ![]() 7dycC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 9418.103 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MPD / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM Sodium acetate pH6.2, 35% MPD, 20% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Apr 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 21779 / % possible obs: 98.6 % / Redundancy: 12.1 % / CC1/2: 0.999 / Net I/σ(I): 29.03 |
Reflection shell | Resolution: 1.21→1.28 Å / Num. unique obs: 2768 / CC1/2: 0.995 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7DU6 Resolution: 1.209→21.896 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 17.36 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.93 Å2 / Biso mean: 22.1422 Å2 / Biso min: 4.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.209→21.896 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|