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- PDB-5d38: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 17... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d38 | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 17 round 7-2 | ||||||
![]() | De novo kemp eliminase KE07 round 7-2 | ||||||
![]() | DE NOVO PROTEIN / LYASE / Kemp Eliminase / Directed Evolution / KE07 | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jackson, C.J. / Hong, N.-S. / Carr, P.D. | ||||||
![]() | ![]() Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 17 round 7-2 Authors: Hong, N.-S. / Jackson, C.J. / Carr, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 101.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.6 KB | Display | ![]() |
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Full document | ![]() | 444.9 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 44.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3iivS ![]() 5d2p ![]() 5d2z ![]() 5d31 ![]() 5d34 ![]() 5d35 ![]() 5d36 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: 29240.377 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b (+) / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 21% (W/V) PEG 3350, 0.1M BIS-TRIS PROPANE, PH 8.5, 0.2M NAF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 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: 1.427→23.41 Å / Num. obs: 100612 / % possible obs: 99.76 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.22 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IIV Resolution: 1.427→23.406 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 20.15 / 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: 1.427→23.406 Å
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Refine LS restraints |
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LS refinement shell |
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