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Open data
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Basic information
Entry | Database: PDB / ID: 8by1 | ||||||
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Title | streptavidin with an iridium catalyst for CH activation | ||||||
![]() | Streptavidin | ||||||
![]() | UNKNOWN FUNCTION / Artificial Metalloenzyme | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Igareta, N.V. / Ward, T.R. | ||||||
Funding support | 1items
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![]() | ![]() Title: streptavidin mutant S112I with an iridium catalyst for CH activation Authors: Igareta, N.V. / 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 | ![]() | 67.4 KB | Display | ![]() |
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PDB format | ![]() | 47.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aqxC ![]() 8by0C ![]() 2bc3S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 13068.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-NOF / | ||||
#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: 2.92 Å3/Da / Density % sol: 57.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 2 M ammonium sulfate 0.1 M sodium acetate (soaking at pH 6.0) |
-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: Sep 11, 2022 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99988 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.486→45.949 Å / Num. obs: 26068 / % possible obs: 99.9 % / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.02 / Rrim(I) all: 0.076 / Net I/σ(I): 23.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BC3 Resolution: 1.486→45.949 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.176 / SU B: 1.119 / SU ML: 0.042 / Average fsc free: 0.9709 / Average fsc work: 0.9766 / Cross valid method: NONE / ESU R: 0.061 / ESU R Free: 0.062 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.472 Å2
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Refinement step | Cycle: LAST / Resolution: 1.486→45.949 Å
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Refine LS restraints |
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LS refinement shell |
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