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Yorodumi- PDB-5kqt: Directed Evolution of Transaminases By Ancestral Reconstruction. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kqt | ||||||
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Title | Directed Evolution of Transaminases By Ancestral Reconstruction. Using Old Proteins for New Chemistries | ||||||
Components | 4-aminoburyrate transaminase | ||||||
Keywords | TRANSFERASE / phylogenetics / directed evolution / transaminase / protein engineering | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. AAC (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Wilding, M. / Newman, J. / Peat, T.S. / Scott, C. | ||||||
Citation | Journal: Green Chemistry / Year: 2017 Title: Reverse engineering: transaminase biocatalyst development using ancestral sequence reconstruction Authors: Wilding, M. / Peat, T.S. / Kalyaanamoorthy, S. / Newman, J. / Scott, C. / Jermiin, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kqt.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kqt.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/5kqt ftp://data.pdbj.org/pub/pdb/validation_reports/kq/5kqt | HTTPS FTP |
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-Related structure data
Related structure data | 5kquC 5kqwC 5kr3C 5kr4C 5kr5C 5kr6C 3gjuS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 51557.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. AAC (bacteria) / Gene: FG99_14885 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A081YAN7, beta-alanine-pyruvate transaminase |
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-Non-polymers , 5 types, 186 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 150 nL plus 150 nL drops of protein at 5 mg/mL and reservoir which consisted of 1.6 M ammonium sulfate, 1% dioxane, 50 mM MES pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→47.8 Å / Num. obs: 32214 / % possible obs: 99.9 % / Redundancy: 20.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.99→2.1 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4.9 / CC1/2: 0.91 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3gju Resolution: 1.99→47.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.621 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.167 / 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: 23.889 Å2
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Refinement step | Cycle: 1 / Resolution: 1.99→47.8 Å
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Refine LS restraints |
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