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- PDB-5z76: Artificial L-threonine 3-dehydrogenase designed by full consensus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5z76 | ||||||
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Title | Artificial L-threonine 3-dehydrogenase designed by full consensus design | ||||||
![]() | Artificial L-threonine 3-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / L-threonine 3-dehydrogenase / full consensus design | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakano, S. / Motoyama, T. / Miyashita, Y. / Ishizuka, Y. / Matsuo, N. / Tokiwa, H. / Shinoda, S. / Asano, Y. / Ito, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data. Authors: Nakano, S. / Motoyama, T. / Miyashita, Y. / Ishizuka, Y. / Matsuo, N. / Tokiwa, H. / Shinoda, S. / Asano, Y. / Ito, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.7 KB | Display | ![]() |
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PDB format | ![]() | 194.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
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Full document | ![]() | 475.5 KB | Display | |
Data in XML | ![]() | 41.3 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z75C ![]() 3wmxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37909.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M ammonium citrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→52.9 Å / Num. obs: 38858 / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.8→2.93 Å / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WMX Resolution: 2.8→52.884 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→52.884 Å
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Refine LS restraints |
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LS refinement shell |
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