[English] 日本語
Yorodumi- PDB-8jqk: Crystal structure of a carbonyl reductase SSCR mutant from Sporob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jqk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a carbonyl reductase SSCR mutant from Sporobolomyces Salmonicolor | ||||||
Components | Aldehyde reductase 2 | ||||||
Keywords | OXIDOREDUCTASE / SSCR / reductase / carbonyl reductase | ||||||
Function / homology | alcohol dehydrogenase (NADP+) / : / alcohol dehydrogenase (NADP+) activity / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / Aldehyde reductase 2 Function and homology information | ||||||
Biological species | Sporobolomyces salmonicolor (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Zhang, H.L. / Li, Q. / Liu, W.D. / Chen, X. / Wu, Q.Q. / Zhu, D.M. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Acs Catalysis / Year: 2023 Title: Engineering a Carbonyl Reductase to Simultaneously Increase Activity Toward Bulky Ketone and Isopropanol for Dynamic Kinetic Asymmetric Reduction via Enzymatic Hydrogen Transfer Authors: Zhang, H. / Chen, X. / Lv, T. / Li, Q. / Liu, W. / Feng, J. / Liu, X. / Yao, P. / Wu, Q. / Zhu, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jqk.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jqk.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 8jqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/8jqk ftp://data.pdbj.org/pub/pdb/validation_reports/jq/8jqk | HTTPS FTP |
---|
-Related structure data
Related structure data | 8jqjC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37586.629 Da / Num. of mol.: 2 / Mutation: M242F/Q245T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sporobolomyces salmonicolor (yeast) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9UUN9, alcohol dehydrogenase (NADP+) #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 6.5, 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→40.1 Å / Num. obs: 76825 / % possible obs: 96.8 % / Redundancy: 7.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.064 / Rrim(I) all: 0.179 / Χ2: 1 / Net I/σ(I): 11.4 / Num. measured all: 585665 |
Reflection shell | Resolution: 1.63→1.67 Å / % possible obs: 95 % / Redundancy: 7.9 % / Rmerge(I) obs: 1.122 / Num. measured all: 44294 / Num. unique obs: 5612 / CC1/2: 0.557 / Rpim(I) all: 0.422 / Rrim(I) all: 1.2 / Χ2: 0.84 / Net I/σ(I) obs: 2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→39.25 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.7 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→39.25 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|