+Open data
-Basic information
Entry | Database: PDB / ID: 7eps | ||||||||||||
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Title | Partial Consensus L-threonine 3-dehydrogenase (E-change) | ||||||||||||
Components | L-threonine 3-dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / L-threonine 3-dehydrogenase / artificial protein | ||||||||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE / THREONINE Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å | ||||||||||||
Authors | Kozuka, K. / Nakano, S. / Asano, Y. / Ito, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Biochemistry / Year: 2021 Title: Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations. Authors: Kozuka, K. / Nakano, S. / Asano, Y. / Ito, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eps.cif.gz | 271 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eps.ent.gz | 210 KB | Display | PDB format |
PDBx/mmJSON format | 7eps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/7eps ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7eps | HTTPS FTP |
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-Related structure data
Related structure data | 7eprC 3wmxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 6 - 315 / Label seq-ID: 26 - 335
NCS ensembles :
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-Components
#1: Protein | Mass: 36819.676 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) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-THR / #4: Chemical | #5: 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: 3.75 Å3/Da / Density % sol: 67.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% [w/v] PEG 3350, 0.2M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.4 Å / Num. obs: 878278 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.1→2.22 Å / Rmerge(I) obs: 0.57 / Num. unique obs: 18253 / CC1/2: 0.895 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMX Resolution: 2.102→49.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.947 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.148 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.893 Å2
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Refinement step | Cycle: LAST / Resolution: 2.102→49.4 Å
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Refine LS restraints |
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