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- PDB-6dc1: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dc1 | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25 round 7 | ||||||
![]() | Kemp eliminase KE07 | ||||||
![]() | LYASE / Kemp Eliminase / Directed Evolution / KE07 / DE NOVO PROTEIN | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 5-nitro-2-oxidanyl-benzenecarbonitrile / DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jackson, C.J. / Hong, N.-S. / Carr, P.D. | ||||||
![]() | ![]() Title: The evolution of multiple active site configurations in a designed enzyme. Authors: Hong, N.S. / Petrovic, D. / Lee, R. / Gryn'ova, G. / Purg, M. / Saunders, J. / Bauer, P. / Carr, P.D. / Lin, C.Y. / Mabbitt, P.D. / Zhang, W. / Altamore, T. / Easton, C. / Coote, M.L. / ...Authors: Hong, N.S. / Petrovic, D. / Lee, R. / Gryn'ova, G. / Purg, M. / Saunders, J. / Bauer, P. / Carr, P.D. / Lin, C.Y. / Mabbitt, P.D. / Zhang, W. / Altamore, T. / Easton, C. / Coote, M.L. / Kamerlin, S.C.L. / Jackson, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 591.5 KB | Display | ![]() |
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PDB format | ![]() | 488.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 120.1 KB | Display | |
Data in CIF | ![]() | 164.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c7hC ![]() 6c7mC ![]() 6c7tC ![]() 6c7vC ![]() 6c8bC ![]() 6caiC ![]() 6ct3C ![]() 6dkvC ![]() 6dnjC ![]() 5d33S 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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12 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 29183.256 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 715 molecules ![](data/chem/img/6VP.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/B3P.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-6VP / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15% PEG3350, 0.1M Bis-trispropane pH 7.5, 0.2M NaF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2017 |
Radiation | Monochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→47.26 Å / Num. obs: 99503 / % possible obs: 99.7 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.189 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.68→2.73 Å / Redundancy: 9.5 % / Rmerge(I) obs: 4.5 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4967 / CC1/2: 0.345 / Rrim(I) all: 4.8 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D33 Resolution: 2.68→47.263 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.57 / 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: 2.68→47.263 Å
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Refine LS restraints |
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LS refinement shell |
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