[English] 日本語
Yorodumi- PDB-5i2g: 1,2-propanediol Dehydration in Roseburia inulinivorans; Structura... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i2g | ||||||
---|---|---|---|---|---|---|---|
Title | 1,2-propanediol Dehydration in Roseburia inulinivorans; Structural Basis for Substrate and Enantiomer Selectivity | ||||||
Components | Diol dehydratase | ||||||
Keywords | LYASE / diol dehydratase / glycyl radical enzymes / enzyme structure | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Roseburia inulinivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.352 Å | ||||||
Authors | LaMattina, J.W. / Reitzer, P. / Kapoor, S. / Galzerani, F. / Koch, D.J. / Gouvea, I.E. / Lanzilotta, W.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: 1,2-Propanediol Dehydration in Roseburia inulinivorans: STRUCTURAL BASIS FOR SUBSTRATE AND ENANTIOMER SELECTIVITY. Authors: LaMattina, J.W. / Keul, N.D. / Reitzer, P. / Kapoor, S. / Galzerani, F. / Koch, D.J. / Gouvea, I.E. / Lanzilotta, W.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5i2g.cif.gz | 321.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5i2g.ent.gz | 268.1 KB | Display | PDB format |
PDBx/mmJSON format | 5i2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/5i2g ftp://data.pdbj.org/pub/pdb/validation_reports/i2/5i2g | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 94114.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Roseburia inulinivorans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1A666 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.125 M sodium acetate, 42 % PEG 400 (w/v), and 0.025 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 74266 / % possible obs: 98.8 % / Redundancy: 7.1 % / CC1/2: 0.929 / Rmerge(I) obs: 0.128 / Rsym value: 0.121 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.35→2.45 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.352→35.357 Å / FOM work R set: 0.8914 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.33 / 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: 94.74 Å2 / Biso mean: 35.63 Å2 / Biso min: 12.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.352→35.357 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|