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Yorodumi- PDB-5yse: Crystal structure of beta-1,2-glucooligosaccharide binding protei... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5yse | |||||||||
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| Title | Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotetraose | |||||||||
Components | Lin1841 protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / solute-binding protein / protein-carbohydrate complex / beta-1 / 2-glucooligosaccharide / sophorooligosaccharide / alpha/beta domain | |||||||||
| Function / homology | Function and homology informationmaltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / metal ion binding Similarity search - Function | |||||||||
| Biological species | Listeria innocua serovar 6a | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Abe, K. / Nakajima, M. / Taguchi, H. / Arakawa, T. / Fushinobu, S. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2018Title: Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua. Authors: Abe, K. / Sunagawa, N. / Terada, T. / Takahashi, Y. / Arakawa, T. / Igarashi, K. / Samejima, M. / Nakai, H. / Taguchi, H. / Nakajima, M. / Fushinobu, S. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5yse.cif.gz | 340.8 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5yse.ent.gz | 277 KB | Display | PDB format |
| PDBx/mmJSON format | 5yse.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/5yse ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5yse | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 5ysbSC ![]() 5ysdC ![]() 5ysfC S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
| #1: Protein | Mass: 44582.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)Strain: ATCC BAA-680 / CLIP 11262 / Gene: lin1841 / Plasmid: pET30a / Production host: ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-MG / | #5: 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: 2.26 Å3/Da / Density % sol: 45.65 % |
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| Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 0.1M MES-NaOH, pH 5.3, 42% (v/v) MPD |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
| Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 28, 2015 |
| Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 1.6→50 Å / Num. obs: 98051 / % possible obs: 96 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Net I/σ(I): 20.7 |
| Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4453 / CC1/2: 0.617 / Rpim(I) all: 0.474 / % possible all: 87 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 5YSB Resolution: 1.6→43.32 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.084 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 46.917 Å2
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| Refinement step | Cycle: 1 / Resolution: 1.6→43.32 Å
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| Refine LS restraints |
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X-RAY DIFFRACTION
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Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria)


