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- PDB-6ss3: Kemp Eliminase HG3.17 mutant Q50K, E47N, N300D Complexed with Tra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ss3 | ||||||
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Title | Kemp Eliminase HG3.17 mutant Q50K, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole | ||||||
![]() | Kemp Eliminase HG3.17 Q50K, E47N, N300D | ||||||
![]() | DE NOVO PROTEIN / Kemp Eliminase / Enzyme / Protein Design | ||||||
Function / homology | Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 6-NITROBENZOTRIAZOLE![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bloch, J.S. / Pinkas, D.M. / Hilvert, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiencyproficiency Authors: Kries, H. / Bloch, J.S. / Bunzel, H.A. / Pinkas, D.M. / Hilvert, 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 | ![]() | 425.5 KB | Display | ![]() |
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PDB format | ![]() | 342.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.8 KB | Display | ![]() |
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Full document | ![]() | 463.1 KB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 48.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6srwC ![]() 6sryC ![]() 6srzC ![]() 6ss1C ![]() 6tu6C ![]() 4bs0S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34462.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.07 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1.1 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE, PH 5.9, SEEDING |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→47.68 Å / Num. obs: 207219 / % possible obs: 99.98 % / Redundancy: 13.2 % / Biso Wilson estimate: 11.8 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.71 |
Reflection shell | Resolution: 1.15→1.191 Å / Num. unique obs: 20488 / CC1/2: 0.483 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BS0 Resolution: 1.15→47.68 Å / SU ML: 0.1126 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.5714 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→47.68 Å
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Refine LS restraints |
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LS refinement shell |
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