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Yorodumi- PDB-7b74: Chimeric Streptavidin With A Dimerization Domain For Artificial T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b74 | ||||||
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Title | Chimeric Streptavidin With A Dimerization Domain For Artificial Transfer Hydrogenation | ||||||
Components | Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin | ||||||
Keywords | METAL BINDING PROTEIN / Artificial tranfer hydrogenation biotin-binding protein artificial metalloenzyme | ||||||
Function / homology | Function and homology information biotin binding / superoxide dismutase / superoxide dismutase activity / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Streptomyces avidinii (bacteria) Mycobacterium bovis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Igareta, N.V. / Ward, T.R. | ||||||
Citation | Journal: Faraday Disc.Chem.Soc / Year: 2023 Title: Spiers Memorial Lecture: Shielding the active site: a streptavidin superoxide-dismutase chimera as a host protein for asymmetric transfer hydrogenation. Authors: Igareta, N.V. / Tachibana, R. / Spiess, D.C. / Peterson, R.L. / 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 | 7b74.cif.gz | 196.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b74.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7b74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b74_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7b74_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7b74_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 7b74_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/7b74 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/7b74 | HTTPS FTP |
-Related structure data
Related structure data | 2bc3S S: Starting model for refinement |
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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
#1: Protein | Mass: 20111.816 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria), (gene. exp.) Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) (bacteria) Strain: ATCC BAA-935 / AF2122/97 / Gene: sodC, BQ2027_MB0440 / Production host: Escherichia coli (E. coli) References: UniProt: P22629, UniProt: P0A609, superoxide dismutase #2: Chemical | ChemComp-4IR / { #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 grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 %w/v PEG 3350 (Polymer) 0.2 M KF (Salt) |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000029 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 12, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.000029 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.85→47.98 Å / Num. obs: 48147 / % possible obs: 98.9 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.1 / Rrim(I) all: 0.188 / Net I/σ(I): 9.2 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bc3 Resolution: 1.85→47.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.883 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.122 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: 24.766 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→47.98 Å
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Refine LS restraints |
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LS refinement shell |
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