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Yorodumi- PDB-7ypd: Discovery and characterization of a new carbonyl reductase from R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ypd | ||||||
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Title | Discovery and characterization of a new carbonyl reductase from Rhodotorula toluroides reducing fluoroketones, and X-ray analysis of the variant by rational engineering | ||||||
Components | Carbonyl reductase | ||||||
Keywords | OXIDOREDUCTASE / Carbonyl reductase / dimer / short-chain-reductase / fluorinated ketone reductase | ||||||
Function / homology | short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / RHTO0S28e01354g1_1 Function and homology information | ||||||
Biological species | Rhodotorula toruloides (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | Watanabe, Y. / Asano, Y. / Hibi, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Discovery and characterization of a new carbonyl reductase from Rhodotorula toluroides reducing fluoroketones, and X-ray analysis of the variant by rational engineering Authors: Watanabe, Y. / Asano, Y. / Hibi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ypd.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ypd.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ypd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ypd_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7ypd_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7ypd_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 7ypd_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/7ypd ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7ypd | HTTPS FTP |
-Related structure data
Related structure data | 3wxbS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26727.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodotorula toruloides (fungus) / Gene: RHTO0S_28e01354g / Production host: Escherichia coli (E. coli) / References: UniProt: A0A061BJP9 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.09 Å3/Da / Density % sol: 41.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris-Hydroxychloride pH8.5, 30%(w/v)PEG4,000, Magnesium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.267→40.56 Å / Num. obs: 106918 / % possible obs: 92.29 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.85 Å2 / Rsym value: 0.067 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.267→1.312 Å / Num. unique obs: 5789 / Rsym value: 0.923 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WXB Resolution: 1.27→40.56 Å / SU ML: 0.1603 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3985 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.27→40.56 Å
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Refine LS restraints |
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LS refinement shell |
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