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- PDB-8qex: Streptavidin variant with a cobalt catalyst for CH metal-catalyze... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qex | ||||||
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Title | Streptavidin variant with a cobalt catalyst for CH metal-catalyzed hydrogen-atom-transfer (M-HAT) | ||||||
![]() | Streptavidin | ||||||
![]() | METAL BINDING PROTEIN / metal-catalyzed hydrogen-atom-transfer / artificial radical cyclase / protein design | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jakob, R.P. / Chen, D. / Ward, T.R. | ||||||
Funding support | 1items
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![]() | ![]() Title: An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway. Authors: Chen, D. / Zhang, X. / Vorobieva, A.A. / Tachibana, R. / Stein, A. / Jakob, R.P. / Zou, Z. / Graf, D.A. / Li, A. / Maier, T. / Correia, B.E. / Ward, T.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.8 KB | Display | ![]() |
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PDB format | ![]() | 49 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 877.7 KB | Display | ![]() |
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Full document | ![]() | 883.4 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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: 17445.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | Mass: 797.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H50CoN6O5S / Feature type: SUBJECT OF INVESTIGATION #3: 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: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.05 M Citric acid, 19 % w/v PEG 1000, 0.1 M Lithium sulfate, 0.05 M Sodium phosphate dibasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.25 Å / Num. obs: 22733 / % possible obs: 98.2 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rpim(I) all: 0.079 / Rrim(I) all: 0.155 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2267 / CC1/2: 0.816 / Rpim(I) all: 0.59 / Rrim(I) all: 1.15 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 25.607 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→45.25 Å
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Refine LS restraints |
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