[English] 日本語
Yorodumi- PDB-5jfn: Crystal structure of Rhodopseudomonas palustris propionaldehyde d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jfn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound CoA and acylated Cys330 | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / acylating aldehyde dehydrogenase / propionylcysteine / bacterial microcompartments | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zarzycki, J. / Sutter, M. / Kerfeld, C.A. | ||||||
Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jfn.cif.gz | 390.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jfn.ent.gz | 311.7 KB | Display | PDB format |
PDBx/mmJSON format | 5jfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jfn_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5jfn_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5jfn_validation.xml.gz | 84.8 KB | Display | |
Data in CIF | 5jfn_validation.cif.gz | 123 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/5jfn ftp://data.pdbj.org/pub/pdb/validation_reports/jf/5jfn | HTTPS FTP |
-Related structure data
Related structure data | 5jflC 5jfmC 4c3sS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 55579.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (strain BisB18) (phototrophic) Strain: BisB18 / Gene: RPC_1174 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21A49 #2: Chemical | ChemComp-1VU / | #3: Chemical | ChemComp-1PE / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM HEPES-NaOH, pH 7.0, 19% w/v PEG4000, 4 mM propionyl-CoA |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.977408 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.2 Å / Num. obs: 162389 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.1 / % possible all: 98.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C3S Resolution: 1.9→39.198 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.12 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.198 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|