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Yorodumi- PDB-6t2l: Streptavidin variants harbouring an artificial organocatalyst bas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t2l | ||||||
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Title | Streptavidin variants harbouring an artificial organocatalyst based cofactor | ||||||
Components | Streptavidin | ||||||
Keywords | biotin-binding protein / artificial cofactor / streptavidin / catalyst | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Lechner, H. / Hocker, B. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Chembiochem / Year: 2021 Title: An Artificial Cofactor Catalyzing the Baylis-Hillman Reaction with Designed Streptavidin as Protein Host*. Authors: Lechner, H. / Emann, V.R. / Breuning, M. / Hocker, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t2l.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t2l.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 6t2l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/6t2l ftp://data.pdbj.org/pub/pdb/validation_reports/t2/6t2l | HTTPS FTP |
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-Related structure data
Related structure data | 6t1eSC 6t1gC 6t1kC 6t2yC 6t2zC 6t30C 6t31C 6t32C 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: 16438.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 |
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#2: Chemical | ChemComp-HL9 / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop Details: 0.17M Na-acetate, 0.085M TRIS-HCl, pH 8.5, 25.5% PEG 4000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1→43.72 Å / Num. obs: 78168 / % possible obs: 99.45 % / Redundancy: 8.5 % / Biso Wilson estimate: 9.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.49 |
Reflection shell | Resolution: 1→1.036 Å / Num. unique obs: 7610 / CC1/2: 0.356 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6t1e Resolution: 1→43.72 Å / SU ML: 0.0948 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.5247
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→43.72 Å
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Refine LS restraints |
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LS refinement shell |
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