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Yorodumi- PDB-6ixm: Crystal structure of the ketone reductase ChKRED20 from the genom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ixm | ||||||
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Title | Crystal structure of the ketone reductase ChKRED20 from the genome of Chryseobacterium sp. CA49 complexed with NAD | ||||||
Components | Short-chain dehydrogenase reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chryseobacterium sp. CA49 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Zhao, F.J. / Jin, Y. / Liu, Z.C. / Wang, G.G. / Wu, Z.L. | ||||||
Citation | Journal: Enzyme Microb. Technol. / Year: 2019 Title: Structure-guided engineering of ChKRED20 from Chryseobacterium sp. CA49 for asymmetric reduction of aryl ketoesters. Authors: Li, T.B. / Zhao, F.J. / Liu, Z. / Jin, Y. / Liu, Y. / Pei, X.Q. / Zhang, Z.G. / Wang, G. / Wu, Z.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ixm.cif.gz | 217.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ixm.ent.gz | 172.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ixm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/6ixm ftp://data.pdbj.org/pub/pdb/validation_reports/ix/6ixm | HTTPS FTP |
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-Related structure data
Related structure data | 4ni5S 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: 26258.797 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chryseobacterium sp. CA49 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: X2D0L0 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M NaCl, 0.1M HEPES, 1.6M (NH4)SO4, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9754 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9754 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.3 Å / Num. obs: 126974 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 6312 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NI5 Resolution: 1.601→29.288 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.601→29.288 Å
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Refine LS restraints |
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LS refinement shell |
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