+Open data
-Basic information
Entry | Database: PDB / ID: 5b5f | ||||||||||||
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Title | Crystal structure of ALiS3-Streptavidin complex | ||||||||||||
Components | Streptavidin | ||||||||||||
Keywords | BIOTIN-BINDING PROTEIN / high-strength agarose hydrogel | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||||||||
Authors | Sugiyama, S. / Terai, T. / Kakinouchi, K. / Fujikake, R. / Nagano, T. / Urano, Y. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Chembiochem / Year: 2017 Title: Improving the Solubility of Artificial Ligands of Streptavidin to Enable More Practical Reversible Switching of Protein Localization in Cells Authors: Tachibana, R. / Terai, T. / Boncompain, G. / Sugiyama, S. / Saito, N. / Perez, F. / Urano, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b5f.cif.gz | 217.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b5f.ent.gz | 176 KB | Display | PDB format |
PDBx/mmJSON format | 5b5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/5b5f ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b5f | HTTPS FTP |
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-Related structure data
Related structure data | 5b5gC 4y59S 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
#1: Protein | Mass: 12693.756 Da / Num. of mol.: 4 / Fragment: UNP residues 40-159 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629 #2: Chemical | ChemComp-6F3 / #3: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M MES-NaOH (pH6.0), 35%(w/v) PEG 1000, 2.0% agarose hydrogel |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→57.27 Å / Num. obs: 134521 / % possible obs: 98 % / Redundancy: 4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.8 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y59 Resolution: 1.2→57.27 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.965 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.043 / 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: 20.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→57.27 Å
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Refine LS restraints |
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