+Open data
-Basic information
Entry | Database: PDB / ID: 7og3 | ||||||
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Title | IRED-88 | ||||||
Components | NAD(P)-dependent oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Imine reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces spectabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å | ||||||
Authors | Faller, M. / Koch, E. | ||||||
Citation | Journal: Acs Catalysis / Year: 2021 Title: Machine-Directed Evolution of an Imine Reductase for Activity and Stereoselectivity Authors: Ma, E.J. / Siirola, E. / Moore, C. / Kummer, A. / Stoeckli, M. / Faller, M. / Bouquet, C. / Eggimann, F. / Ligibel, M. / Huynh, D. / Cutler, G. / Siegrist, L. / Lewis, R.A. / Acker, A.C. / ...Authors: Ma, E.J. / Siirola, E. / Moore, C. / Kummer, A. / Stoeckli, M. / Faller, M. / Bouquet, C. / Eggimann, F. / Ligibel, M. / Huynh, D. / Cutler, G. / Siegrist, L. / Lewis, R.A. / Acker, A.C. / Freund, E. / Koch, E. / Vogel, M. / Schlingensiepen, H. / Oakeley, E.J. / Snajdrova, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7og3.cif.gz | 231.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7og3.ent.gz | 184.2 KB | Display | PDB format |
PDBx/mmJSON format | 7og3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/7og3 ftp://data.pdbj.org/pub/pdb/validation_reports/og/7og3 | HTTPS FTP |
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-Related structure data
Related structure data | 3zgyS 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: 34021.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces spectabilis (bacteria) / Gene: CP982_37880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5P2XKZ4 #2: Chemical | #3: Chemical | #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 Å3/Da / Density % sol: 38.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.1M HEPES, 1.39M Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→59.72 Å / Num. obs: 43308 / % possible obs: 99.88 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 9.44 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.286 / Num. unique obs: 4218 / CC1/2: 0.894 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZGY Resolution: 1.904→59.72 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.171 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.145
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Displacement parameters | Biso mean: 28.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.904→59.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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