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Yorodumi- PDB-7ejh: Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ejh | ||||||
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Title | Crystal structure of KRED mutant-F147L/L153Q/Y190P/L199A/M205F/M206F and 2-hydroxyisoindoline-1,3-dione complex | ||||||
Components | 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Ketoreductases / NADPH-dependent / Enantioselectivity | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Lactobacillus kefiri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72883927603 Å | ||||||
Authors | Cui, J. / Huang, X. / Wang, B. / Zhao, H. / Zhou, J. | ||||||
Citation | Journal: Nat Catal / Year: 2022 Title: Photoinduced chemomimetic biocatalysis for enantioselective intermolecular radical conjugate addition Authors: Huang, X. / Feng, J. / Cui, J. / Jiang, G. / Harrison, W. / Zang, X. / Zhou, J. / Wang, B. / Zhao, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ejh.cif.gz | 239.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ejh.ent.gz | 175.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ejh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/7ejh ftp://data.pdbj.org/pub/pdb/validation_reports/ej/7ejh | HTTPS FTP |
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-Related structure data
Related structure data | 7ejiC 7ejjC 7vdoC 7ve7C 4rf2S S: Starting model for refinement C: citing same article (ref.) |
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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: 26773.164 Da / Num. of mol.: 4 / Mutation: F147L, L153Q, Y190P, L199A, M205F, M206F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus kefiri (bacteria) / Gene: adhR, fabG3, DNL43_05835, LKE01_04370 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q6WVP7 #2: Chemical | #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-J66 / #5: 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: 2.17 Å3/Da / Density % sol: 43.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 30% (w/v) PEG 2000 MME, 0.1 M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97855 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 93853 / % possible obs: 98.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.3160424274 Å2 / CC1/2: 0.914 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.73→1.76 Å / Rmerge(I) obs: 0.507 / Num. unique obs: 93853 / CC1/2: 0.917 / Rsym value: 0.507 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RF2 Resolution: 1.72883927603→41.7340655768 Å / SU ML: 0.232614047856 / Cross valid method: FREE R-VALUE / σ(F): 1.3437467371 / Phase error: 28.0584998069 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: 22.9078282165 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72883927603→41.7340655768 Å
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Refine LS restraints |
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LS refinement shell |
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