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- PDB-5d2y: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 7 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d2y | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 7 Round 5 | ||||||
![]() | De novo designed kemp eliminase KE07 | ||||||
![]() | 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 7 Round 5 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 | ![]() | 67.1 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 430.9 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rkxS ![]() 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 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) / Plasmid: pET29b (+) / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 25mM HEPES, pH 7.25, 0.1M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.984→19.64 Å / Num. obs: 31217 / % possible obs: 99.51 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.1149 / Net I/σ(I): 24.47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RKX Resolution: 1.984→19.639 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.21 / 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: 1.984→19.639 Å
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Refine LS restraints |
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LS refinement shell |
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