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Yorodumi- PDB-5wuw: Serratia marcescens short-chain dehydrogenase/reductase F98L/F202... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wuw | ||||||
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Title | Serratia marcescens short-chain dehydrogenase/reductase F98L/F202L mutant | ||||||
Components | Short-chain dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Serratia marcescens short-chain dehydrogenase/reductase / SmSDR / F98Y/F202Y mutant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Liu, J.-S. / Tsou, Y. / Wang, W.-C. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Structure-guided design of Serratia marcescens short-chain dehydrogenase/reductase for stereoselective synthesis of (R)-phenylephrine. Authors: Liu, J.-S. / Kuan, Y.-C. / Tsou, Y. / Lin, T.-Y. / Hsu, W.-H. / Yang, M.-T. / Lin, J.-Y. / Wang, W.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wuw.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wuw.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 5wuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/5wuw ftp://data.pdbj.org/pub/pdb/validation_reports/wu/5wuw | HTTPS FTP |
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-Related structure data
Related structure data | 5wulC 5wvaC 4zgwS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29585.332 Da / Num. of mol.: 2 / Mutation: F98L/F202L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A192ICX3 #2: Chemical | ChemComp-NAP / | #3: 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: 1.72 Å3/Da / Density % sol: 28.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM HEPES buffer (pH 7.0), 40% (v/v) tacsimate (pH 7.0), 2 mM spermine, and 2 mM hexamine cobalt (III) chloride |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 33651 / % possible obs: 92.3 % / Redundancy: 26.7 % / Net I/σ(I): 10.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZGW Resolution: 1.9→50.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.062 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.543 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50.01 Å
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Refine LS restraints |
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