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- PDB-3iiv: Evolutionary optimization of computationally designed enzymes: Ke... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3iiv | ||||||
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Title | Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series | ||||||
![]() | KE7 KE7_R7_1/3H | ||||||
![]() | LYASE / beta barrel | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khersonsky, O. / Dym, O. / Tawfik, D.S. | ||||||
![]() | ![]() Title: Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series. Authors: Khersonsky, O. / Rothlisberger, D. / Dym, O. / Albeck, S. / Jackson, C.J. / 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 | ![]() | 115.9 KB | Display | ![]() |
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PDB format | ![]() | 89.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 439.6 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3iioC ![]() 3iipSC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 3 - 250 / Label seq-ID: 3 - 250
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Components
#1: Protein | Mass: 29052.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 292 K / Method: microbatch under oil / pH: 8 Details: 0.2M MgCl2, Tris pH8, 20% PEG6000, Microbatch under oil, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2007 |
Radiation | Monochromator: Mirror 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 52231 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3IIP Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 2.49 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.886 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1915 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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