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- PDB-5kr3: Directed Evolution of Transaminases By Ancestral Reconstruction. ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kr3 | ||||||
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Title | Directed Evolution of Transaminases By Ancestral Reconstruction. Using Old Proteins for New Chemistries | ||||||
![]() | 4-aminobutyrate transaminase | ||||||
![]() | TRANSFERASE / phylogenetics / directed evolution / transaminase / protein engineering | ||||||
Function / homology | Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / PYRIDOXAL-5'-PHOSPHATE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilding, M. / Newman, J. / Peat, T.S. / Scott, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195 KB | Display | ![]() |
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PDB format | ![]() | 153 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.3 KB | Display | ![]() |
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Full document | ![]() | 459.5 KB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 53.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kqtSC ![]() 5kquC ![]() 5kqwC ![]() 5kr4C ![]() 5kr5C ![]() 5kr6C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 459 / Label seq-ID: 22 - 479
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Components
#1: Protein | Mass: 52048.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 150 plus 150 nL drops with protein at 10 mg/mL and reservoir conditions of 20% PEG 3350, 135 mM ammonium formate. Microseeds were used for nucleation. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→41.9 Å / Num. obs: 63517 / % possible obs: 98.9 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 7 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.965 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5kqt Resolution: 1.95→41.9 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.844 / SU B: 4.033 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.186 / 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: 18.225 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→41.9 Å
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Refine LS restraints |
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