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Yorodumi- PDB-5jfm: Crystal structure of Rhodopseudomonas palustris propionaldehyde d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jfm | ||||||
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Title | Crystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound propionyl-CoA | ||||||
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: 2.516 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jfm.cif.gz | 684.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jfm.ent.gz | 564 KB | Display | PDB format |
PDBx/mmJSON format | 5jfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jfm_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5jfm_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5jfm_validation.xml.gz | 137.1 KB | Display | |
Data in CIF | 5jfm_validation.cif.gz | 183.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/5jfm ftp://data.pdbj.org/pub/pdb/validation_reports/jf/5jfm | HTTPS FTP |
-Related structure data
Related structure data | 5jflC 5jfnC 4c3sS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55523.531 Da / Num. of mol.: 8 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-COA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.516→39.259 Å
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Refine LS restraints |
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LS refinement shell |
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