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Yorodumi- PDB-8qex: Streptavidin variant with a cobalt catalyst for CH metal-catalyze... -
+Open data
-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) | ||||||
Components | Streptavidin | ||||||
Keywords | METAL BINDING PROTEIN / metal-catalyzed hydrogen-atom-transfer / artificial radical cyclase / protein design | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Jakob, R.P. / Chen, D. / Ward, T.R. | ||||||
Funding support | 1items
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Citation | Journal: Nat.Chem. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qex.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qex.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 8qex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qex_validation.pdf.gz | 877.7 KB | Display | wwPDB validaton report |
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Full document | 8qex_full_validation.pdf.gz | 883.4 KB | Display | |
Data in XML | 8qex_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 8qex_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/8qex ftp://data.pdbj.org/pub/pdb/validation_reports/qe/8qex | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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: 17445.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22629 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.978 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.155 / 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: 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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