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Yorodumi- PDB-5gws: 4-hydroxyisoleucine dehydrogenase complexed with NADH and succinate -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gws | ||||||
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Title | 4-hydroxyisoleucine dehydrogenase complexed with NADH and succinate | ||||||
Components | 4-hydroxyisolecuine dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NADH-dependent / short-chain / dehydrogenase / reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus thuringiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Shi, X. / Miyakawa, T. / Nakamura, A. / Tanokura, M. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Engineering a short-chain dehydrogenase/reductase for the stereoselective production of (2S,3R,4S)-4-hydroxyisoleucine with three asymmetric centers. Authors: Shi, X. / Miyakawa, T. / Nakamura, A. / Hou, F. / Hibi, M. / Ogawa, J. / Kwon, Y. / Tanokura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gws.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gws.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gws_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5gws_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5gws_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 5gws_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/5gws ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gws | HTTPS FTP |
-Related structure data
Related structure data | 5gwrC 5gwtC 3f9iS C: citing same article (ref.) 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: 31386.279 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: 2e2 / Gene: AC241_05390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0Q8K4 #2: Chemical | ChemComp-NAD / #3: Chemical | #4: 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: 3.32 Å3/Da / Density % sol: 62.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.0M ammonium sulfate, 0.1M citrate (pH 5.5) |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. obs: 66938 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2.35→2.39 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F9I Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.36 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.201 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.093 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→20 Å
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Refine LS restraints |
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