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Yorodumi- PDB-6y2m: Streptavidin mutant S112R with a biotC4-1 cofactor - an artificia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y2m | ||||||||||||||||||
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Title | Streptavidin mutant S112R with a biotC4-1 cofactor - an artificial iron hydroxylase | ||||||||||||||||||
Components | Streptavidin | ||||||||||||||||||
Keywords | OXIDOREDUCTASE / Artificial Metalloenzyme / Iron Hydroxylase / Biotin-Binding Protein | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||||||||
Authors | Serrano-Plana, J. / Rumo, C. / Rebelein, J.G. / Peterson, R.L. / Barnet, M. / Ward, T.R. | ||||||||||||||||||
Funding support | Switzerland, European Union, Germany, 5items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Enantioselective Hydroxylation of Benzylic C(sp3)-H Bonds by an Artificial Iron Hydroxylase Based on the Biotin-Streptavidin Technology. Authors: Serrano-Plana, J. / Rumo, C. / Rebelein, J.G. / Peterson, R.L. / Barnet, M. / 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 | 6y2m.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y2m.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6y2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y2m_validation.pdf.gz | 725.2 KB | Display | wwPDB validaton report |
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Full document | 6y2m_full_validation.pdf.gz | 728.2 KB | Display | |
Data in XML | 6y2m_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 6y2m_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/6y2m ftp://data.pdbj.org/pub/pdb/validation_reports/y2/6y2m | HTTPS FTP |
-Related structure data
Related structure data | 6y25C 6y2tC 6y33C 6y34C 6y3qC 3pk2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 16639.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P22629 |
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#2: Chemical | ChemComp-O6T / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4 |
-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: Apr 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45.69 Å / Num. obs: 11549 / % possible obs: 100 % / Redundancy: 24.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 26 % / Rmerge(I) obs: 1.9 / Num. unique obs: 797 / CC1/2: 0.907 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3pk2 Resolution: 1.95→45.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.143 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.149 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→45.64 Å
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Refine LS restraints |
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LS refinement shell |
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