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Yorodumi- PDB-5ysb: Crystal structure of beta-1,2-glucooligosaccharide binding protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ysb | ||||||
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Title | Crystal structure of beta-1,2-glucooligosaccharide binding protein in ligand-free form | ||||||
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 information 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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Abe, K. / Nakajima, M. / Taguchi, H. / Arakawa, T. / Fushinobu, S. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ysb.cif.gz | 315.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ysb.ent.gz | 254.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ysb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ysb_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 5ysb_full_validation.pdf.gz | 460.7 KB | Display | |
Data in XML | 5ysb_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 5ysb_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/5ysb ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5ysb | HTTPS FTP |
-Related structure data
Related structure data | 5ysdC 5yseC 5ysfC 3uorS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 36 - 419 / Label seq-ID: 11 - 394
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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: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92AS8 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.15M zinc acetate, 15% (w/v) PEG 3350 |
-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: Jun 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: 2.2→50 Å / Num. obs: 38141 / % possible obs: 98.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.047 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.571 / Num. unique obs: 1912 / CC1/2: 0.906 / Rpim(I) all: 0.263 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UOR Resolution: 2.2→19.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.858 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.23 / 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: 49.947 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→19.24 Å
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Refine LS restraints |
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