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- PDB-5ysd: 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: 5ysd | |||||||||
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Title | Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose | |||||||||
![]() | Lin1841 protein | |||||||||
![]() | SUGAR BINDING PROTEIN / solute-binding protein / protein-carbohydrate complex / beta-1 / 2-glucooligosaccharide / sophorooligosaccharide / alpha/beta domain | |||||||||
Function / homology | ![]() maltose 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 | ![]() ![]() ![]() | |||||||||
![]() | Abe, K. / Nakajima, M. / Taguchi, H. / Arakawa, T. / Fushinobu, S. | |||||||||
![]() | ![]() Title: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.3 KB | Display | ![]() |
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PDB format | ![]() | 271.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 32.2 KB | Display | |
Data in CIF | ![]() | 45.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ysbC ![]() 5yseSC ![]() 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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1 | ![]()
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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.) ![]() Strain: ATCC BAA-680 / CLIP 11262 / Gene: lin1841 / Plasmid: pET30a / Production host: ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.15M MES-NaOH, pH 5.5, 50% (v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 19, 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: 2.1→50 Å / Num. obs: 44909 / % possible obs: 96.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.071 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.639 / Num. unique obs: 2234 / CC1/2: 0.697 / Rpim(I) all: 0.389 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YSE Resolution: 2.1→44.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.176 / 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: 56.682 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→44.95 Å
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Refine LS restraints |
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