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- PDB-6t1k: Streptavidin variants harbouring an artificial organocatalyst bas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t1k | ||||||
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Title | Streptavidin variants harbouring an artificial organocatalyst based cofactor | ||||||
![]() | Streptavidin | ||||||
![]() | Biotin-binding protein / artificial cofactor / streptavidin / catalyst | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lechner, H. / Hocker, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An Artificial Cofactor Catalyzing the Baylis-Hillman Reaction with Designed Streptavidin as Protein Host*. Authors: Lechner, H. / Emann, V.R. / Breuning, M. / Hocker, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.3 KB | Display | ![]() |
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PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 671.2 KB | Display | ![]() |
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Full document | ![]() | 671.6 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t1eSC ![]() 6t1gC ![]() 6t2lC ![]() 6t2yC ![]() 6t2zC ![]() 6t30C ![]() 6t31C ![]() 6t32C 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16495.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-HL9 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: CHES 0.1 M pH 9.5 30% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→43.75 Å / Num. obs: 46054 / % possible obs: 99.79 % / Redundancy: 10.7 % / Biso Wilson estimate: 14.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.47 |
Reflection shell | Resolution: 1.2→1.24 Å / Num. unique obs: 4461 / CC1/2: 0.301 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6T1E Resolution: 1.2→43.75 Å / SU ML: 0.145 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1909
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→43.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.9453499643 Å / Origin y: 24.4919537299 Å / Origin z: -3.090870903 Å
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Refinement TLS group | Selection details: all |