[English] 日本語
![](img/lk-miru.gif)
- PDB-5jfm: Crystal structure of Rhodopseudomonas palustris propionaldehyde d... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5jfm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound propionyl-CoA | ||||||
![]() | Aldehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / acylating aldehyde dehydrogenase / propionylcysteine / bacterial microcompartments | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zarzycki, J. / Sutter, M. / Kerfeld, C.A. | ||||||
![]() | ![]() Title: In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment. Authors: Zarzycki, J. / Sutter, M. / Cortina, N.S. / Erb, T.J. / Kerfeld, C.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 684.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 564 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 137.1 KB | Display | |
Data in CIF | ![]() | 183.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jflC ![]() 5jfnC ![]() 4c3sS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 55523.531 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: BisB18 / Gene: RPC_1174 / Production host: ![]() ![]() #2: Chemical | ChemComp-1VU / #3: Chemical | ChemComp-COA / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 50 mM sodium citrate, pH 4.8, 4% w/v PEG8000, 5 mM propionyl-CoA |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.516→39.26 Å / Num. obs: 135429 / % possible obs: 95.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.52→2.65 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.3 / % possible all: 91.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4C3S Resolution: 2.516→39.259 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.25
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.516→39.259 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|