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Yorodumi- PDB-7eji: Crystal structure of KRED F147L/L153Q/Y190P/L199A/M205F/M206F var... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eji | ||||||
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Title | Crystal structure of KRED F147L/L153Q/Y190P/L199A/M205F/M206F variant and methyl methacrylate 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: 1.56001602495 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 | 7eji.cif.gz | 239.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eji.ent.gz | 175.2 KB | Display | PDB format |
PDBx/mmJSON format | 7eji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eji_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 7eji_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7eji_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 7eji_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/7eji ftp://data.pdbj.org/pub/pdb/validation_reports/ej/7eji | HTTPS FTP |
-Related structure data
Related structure data | 7ejhC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#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 |
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-Non-polymers , 9 types, 663 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NAP / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PEG / | #10: Water | ChemComp-HOH / | |
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-Details
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: 2.1 Å3/Da / Density % sol: 41.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→62.25 Å / Num. obs: 137332 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.9084709456 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.032 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.52→1.54 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6583 / CC1/2: 0.712 / Rpim(I) all: 0.677 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RF2 Resolution: 1.56001602495→50.6890640226 Å / SU ML: 0.17923616796 / Cross valid method: FREE R-VALUE / σ(F): 1.35011065855 / Phase error: 24.7491095516 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: 28.6000927283 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56001602495→50.6890640226 Å
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Refine LS restraints |
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LS refinement shell |
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