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Yorodumi- PDB-6t1e: Streptavidin variants harbouring an artificial organocatalyst bas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t1e | ||||||
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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: 1.3 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 | 6t1e.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t1e.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 6t1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/6t1e ftp://data.pdbj.org/pub/pdb/validation_reports/t1/6t1e | HTTPS FTP |
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-Related structure data
Related structure data | 6t1gC 6t1kC 6t2lC 6t2yC 6t2zC 6t30C 6t31C 6t32C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16598.053 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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-Non-polymers , 5 types, 120 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-HL9 / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: (NH4)2SO4 1.8 M, NaCH3COO 0.1 M, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→29.76 Å / Num. obs: 36595 / % possible obs: 99.92 % / Redundancy: 14.4 % / Biso Wilson estimate: 17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08801 / Rpim(I) all: 0.02393 / Rrim(I) all: 0.09129 / Net I/σ(I): 18.71 |
Reflection shell | Resolution: 1.3→1.346 Å / Num. unique obs: 3573 / CC1/2: 0.398 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→29.76 Å / SU ML: 0.1288 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1802 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→29.76 Å
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Refine LS restraints |
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LS refinement shell |
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