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Yorodumi- PDB-5wul: Serratia marcescens short-chain dehydrogenase/reductase F98A/F202L -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wul | ||||||
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Title | Serratia marcescens short-chain dehydrogenase/reductase F98A/F202L | ||||||
Components | Short-chain dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Serratia marcescens short-chain dehydrogenase/reductase / SmSDR / F98A/F202L | ||||||
Function / homology | Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Short-chain dehydrogenase Function and homology information | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 | 5wul.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wul.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/5wul ftp://data.pdbj.org/pub/pdb/validation_reports/wu/5wul | HTTPS FTP |
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-Related structure data
Related structure data | 5wuwC 5wvaC 4zgwS S: Starting model for refinement C: citing same article (ref.) |
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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: 29543.250 Da / Num. of mol.: 2 / Mutation: F98A/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: 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: 1.7 Å3/Da / Density % sol: 27.53 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 Details: 50mM HEPES buffer (pH 7.0), 40% (v/v) tacsimate (pH 7.0), 2mM spermine, 2mM 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: Mar 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→67.58 Å / Num. obs: 34418 / % possible obs: 99.5 % / Redundancy: 13.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.014 / Rsym value: 0.053 / Net I/σ(I): 44.7 |
Reflection shell | Resolution: 1.87→1.94 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZGW Resolution: 1.87→67.58 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.335 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.122 / 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: 20.61 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→67.58 Å
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Refine LS restraints |
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