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- PDB-6dnj: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dnj | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 28 round 5 | ||||||
![]() | Kemp eliminase KE07 | ||||||
![]() | LYASE / Directed Evolution / DE NOVO PROTEIN | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 5-nitro-1,2-benzoxazole![]() | ||||||
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 | ![]() | 128.3 KB | Display | ![]() |
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PDB format | ![]() | 98.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 868.5 KB | Display | ![]() |
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Full document | ![]() | 869.1 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6c7hC ![]() 6c7mC ![]() 6c7tC ![]() 6c7vC ![]() 6c8bC ![]() 6caiC ![]() 6ct3C ![]() 6dc1C ![]() 6dkvC ![]() 5c7mS 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29328.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MPD / ( |
#3: Chemical | ChemComp-H5J / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: 25 mM HEPES, pH 7.25, 0.1 M NaCl |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 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: 1.65→42 Å / Num. obs: 52414 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.13 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 8.7 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2555 / CC1/2: 0.38 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5C7M Resolution: 1.65→43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.766 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.065 / 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: 27.921 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→43 Å
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Refine LS restraints |
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