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- PDB-3q2d: Optimization of the in silico designed Kemp eliminase KE70 by com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q2d | ||||||
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Title | Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution | ||||||
![]() | Deoxyribose phosphate aldolase | ||||||
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Function / homology | Aldolase class I / ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Khersonsky, O. / Rothlisberge, D. / Wollacott, A.M. / Murphy, P. / Dym, O. / Albeck, S. / Kiss, G. / Houk, K.N. / Baker, D. / Tawfik, D.S. / Israel Structural Proteomics Center (ISPC) | ||||||
![]() | ![]() Title: Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution Authors: Khersonsky, O. / Rothlisberger, D. / Wollacott, A.M. / Murphy, P. / Dym, O. / Albeck, S. / Kiss, G. / Houk, K.N. / Baker, D. / Tawfik, D.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 | ![]() | 98.8 KB | Display | ![]() |
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PDB format | ![]() | 74.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3npuC ![]() 3npvC ![]() 3npwC ![]() 3npxC ![]() 3nq2C ![]() 3nq8C ![]() 3nqvC ![]() 3nr0C ![]() 3nrqS C: citing same article ( S: Starting model for refinement |
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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: 28918.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.96 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M NaMalonate, Imidazole, Boric acid pH4, 25% PEG 1500 , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.19→50 Å / Num. all: 28757 / Num. obs: 27722 / % possible obs: 96.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.19→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.342 / % possible all: 79.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3NRQ Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.942 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R Free: 0.229 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.622 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.247 Å / Total num. of bins used: 20
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