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Yorodumi- PDB-7cgv: Full consensus L-threonine 3-dehydrogenase, FcTDH-IIYM (NAD+ boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cgv | |||||||||
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Title | Full consensus L-threonine 3-dehydrogenase, FcTDH-IIYM (NAD+ bound form) | |||||||||
Components | Artificial L-threonine 3-dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / L-Threonine 3-dehydrogenase / Artificial protein / Full consensus design | |||||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | |||||||||
Authors | Motoyama, T. / Hiramatsu, N. / Asano, Y. / Nakano, S. / Ito, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Biochemistry / Year: 2020 Title: Protein Sequence Selection Method That Enables Full Consensus Design of Artificial l-Threonine 3-Dehydrogenases with Unique Enzymatic Properties. Authors: Motoyama, T. / Hiramatsu, N. / Asano, Y. / Nakano, S. / Ito, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cgv.cif.gz | 317.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cgv.ent.gz | 207.4 KB | Display | PDB format |
PDBx/mmJSON format | 7cgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cgv_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7cgv_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7cgv_validation.xml.gz | 49 KB | Display | |
Data in CIF | 7cgv_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/7cgv ftp://data.pdbj.org/pub/pdb/validation_reports/cg/7cgv | HTTPS FTP |
-Related structure data
Related structure data | 3wmxS 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: 37921.344 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: L-threonine 3-dehydrogenase #2: Chemical | ChemComp-NAD / #3: 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: 43.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 2.5mM NAD+, 12% PEG 3350, 0.1M sodium acetate trihydrate (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→36.41 Å / Num. obs: 48940 / % possible obs: 96.17 % / Redundancy: 3.4 % / Biso Wilson estimate: 43.67 Å2 / CC1/2: 0.985 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.38→2.47 Å / Num. unique obs: 4236 / CC1/2: 0.985 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMX Resolution: 2.38→36.41 Å / SU ML: 0.3694 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.1435 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: 50.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→36.41 Å
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Refine LS restraints |
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LS refinement shell |
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