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Yorodumi- PDB-5z75: Artificial L-threonine 3-dehydrogenase designed by ancestral sequ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z75 | ||||||
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Title | Artificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction. | ||||||
Components | Artificial L-threonine 3-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ancestral sequence reconstruction / L-threonine 3-dehydrogenase | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nakano, S. / Motoyama, T. / Miyashita, Y. / Ishizuka, Y. / Matsuo, N. / Tokiwa, H. / Shinoda, S. / Asano, Y. / Ito, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochemistry / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z75.cif.gz | 269.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z75.ent.gz | 216.5 KB | Display | PDB format |
PDBx/mmJSON format | 5z75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z75_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5z75_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5z75_validation.xml.gz | 52.6 KB | Display | |
Data in CIF | 5z75_validation.cif.gz | 72.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/5z75 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/5z75 | HTTPS FTP |
-Related structure data
Related structure data | 5z76C 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: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 37009.844 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 | #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: 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: 2.17 Å3/Da / Density % sol: 43.37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M potassium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2017 |
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→92.7 Å / Num. obs: 73459 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 3652 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WMX Resolution: 2.1→92.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.52 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.195 / 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: 36.065 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→92.7 Å
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Refine LS restraints |
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