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- PDB-5h6u: Structure of alginate-binding protein AlgQ2 in complex with an al... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h6u | |||||||||
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Title | Structure of alginate-binding protein AlgQ2 in complex with an alginate pentasaccharide | |||||||||
![]() | AlgQ2 | |||||||||
![]() | SUGAR BINDING PROTEIN / Alginate oligosaccharide / closed conformation / Solute-binding protein / Sphingomonas | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Uenishi, K. / Kaneko, A. / Maruyama, Y. / Mikami, B. / Murata, K. / Hashimoto, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate Authors: Kaneko, A. / Uenishi, K. / Maruyama, Y. / Mizuno, N. / Baba, S. / Kumasaka, T. / Mikami, B. / 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 | ![]() | 225.9 KB | Display | ![]() |
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PDB format | ![]() | 179.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 942.6 KB | Display | ![]() |
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Full document | ![]() | 951.3 KB | Display | |
Data in XML | ![]() | 42 KB | Display | |
Data in CIF | ![]() | 61.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xigC ![]() 4xtcC ![]() 5h71C ![]() 1j1nS 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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Unit cell |
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Components
#1: Protein | Mass: 57251.715 Da / Num. of mol.: 2 / Fragment: UNP residues 28-514 / Mutation: R253K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.07 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG4000, 0.2 M calcium chloride, 0.1 M tris(hydroxymethyl)aminomethan-hydrochloride acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 56452 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 31.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.6 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J1N Resolution: 2.006→35.68 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.65 / 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: 2.006→35.68 Å
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Refine LS restraints |
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LS refinement shell |
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