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Yorodumi- PDB-7emg: Carbonyl Reductase Variant 4 (R123C/L209P/F183Y/V61K) from Serrat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7emg | ||||||
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Title | Carbonyl Reductase Variant 4 (R123C/L209P/F183Y/V61K) from Serratia marcescens complexed with NADP+ | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] reductase | ||||||
Keywords | OXIDOREDUCTASE / NADP+ complex / carbonyl reductase | ||||||
Function / homology | Function and homology information : / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.449 Å | ||||||
Authors | Zheng, Y.C. / Wang, T. / Bai, Y.P. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2021 Title: Stereoselective synthesis of chiral delta-lactones via an engineered carbonyl reductase. Authors: Wang, T. / Zhang, X.Y. / Zheng, Y.C. / Bai, Y.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7emg.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7emg.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 7emg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7emg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7emg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7emg_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 7emg_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/7emg ftp://data.pdbj.org/pub/pdb/validation_reports/em/7emg | HTTPS FTP |
-Related structure data
Related structure data | 1q7cS 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
#1: Protein | Mass: 26624.428 Da / Num. of mol.: 2 / Mutation: V61K, R123C, F183Y, L209P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) Gene: fabG, A8A12_06940, AR325_11665, BVG93_06205, G3M86_05635, G3M87_05635, G3M88_05635, G3M89_05635, GV243_09700, HMI62_09690 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0G8B235, 3-oxoacyl-[acyl-carrier-protein] reductase #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.18 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Potassium sodium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Imidazole; 0.1M MES monohydrate ...Details: 0.1M Sodium formate; 0.1M Ammonium acetate; 0.1M Sodium citrate tribasic dihydrate; 0.1M Potassium sodium tartrate tetrahydrate; 0.1M Sodium oxamate; 0.1M Imidazole; 0.1M MES monohydrate (acid); pH 6.5; 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.449→50 Å / Num. obs: 17156 / % possible obs: 99 % / Redundancy: 12.8 % / Biso Wilson estimate: 33.5 Å2 / CC1/2: 0.969 / CC star: 0.992 / Χ2: 0.878 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.449→2.49 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 849 / CC1/2: 0.954 / CC star: 0.988 / Χ2: 1.016 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1q7c Resolution: 2.449→42.596 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML
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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 max: 115.79 Å2 / Biso mean: 35.7916 Å2 / Biso min: 15.51 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.449→42.596 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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