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- PDB-5gx6: Crystal structure of solute-binding protein complexed with unsatu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gx6 | ||||||||||||
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Title | Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with a sulfate group at C-4 position of GalNAc | ||||||||||||
![]() | Extracellular solute-binding protein family 1 | ||||||||||||
![]() | SUGAR BINDING PROTEIN / glycosaminoglycan / ABC transporter / solute-binding protein | ||||||||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Extracellular solute-binding protein family 1![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A bacterial ABC transporter enables import of mammalian host glycosaminoglycans Authors: Oiki, S. / Mikami, B. / Maruyama, Y. / Murata, K. / Hashimoto, W. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 322 KB | Display | ![]() |
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PDB format | ![]() | 257.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 60.9 KB | Display | |
Data in CIF | ![]() | 89.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gubSC ![]() 5gx7C ![]() 5gx8C C: citing same article ( S: Starting model for refinement |
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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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55245.367 Da / Num. of mol.: 3 / Fragment: UNP residues 19-500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 12112 / Gene: Smon_0123 / Production host: ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium chloride, 0.1M HEPES (pH 7.0), 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. obs: 136919 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 37.5 |
Reflection shell | Resolution: 1.81→1.84 Å / Rmerge(I) obs: 0.519 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GUB Resolution: 1.81→39.453 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→39.453 Å
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Refine LS restraints |
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LS refinement shell |
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