+Open data
-Basic information
Entry | Database: PDB / ID: 4y5d | ||||||
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Title | CRYSTAL STRUCTURE OF ALiS2-STREPTAVIDIN COMPLEX | ||||||
Components | Streptavidin | ||||||
Keywords | BIOTIN-BINDING PROTEIN / Inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å | ||||||
Authors | Sugiyama, S. / Terai, T. / Kohno, M. / Ishida, H. / Nagano, T. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport Authors: Terai, T. / Kohno, M. / Boncompain, G. / Sugiyama, S. / Saito, N. / Fujikake, R. / Ueno, T. / Komatsu, T. / Hanaoka, K. / Okabe, T. / Urano, Y. / Perez, F. / Nagano, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y5d.cif.gz | 224 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y5d.ent.gz | 180 KB | Display | PDB format |
PDBx/mmJSON format | 4y5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/4y5d ftp://data.pdbj.org/pub/pdb/validation_reports/y5/4y5d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 12851.911 Da / Num. of mol.: 4 / Fragment: UNP residues 39-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Streptomyces avidinii (bacteria) / References: UniProt: P22629 |
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-Non-polymers , 5 types, 420 molecules
#2: Chemical | #3: Chemical | ChemComp-PE3 / | #4: Chemical | ChemComp-DMS / | #5: Chemical | #6: 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: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M Mes-NaOH (pH6.0), 45%(w/v) PEG1000 / PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 132391 / % possible obs: 98.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.7 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.649 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / 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: 16.943 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→50 Å
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Refine LS restraints |
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