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- PDB-1oge: The Structure of Bacillus subtilis RbsD complexed with Ribose 5-p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oge | |||||||||
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Title | The Structure of Bacillus subtilis RbsD complexed with Ribose 5-phosphate | |||||||||
![]() | HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD | |||||||||
![]() | TRANSPORT / RIBOSE 5-PHOSPHATE / SUGAR TRANSPORT | |||||||||
Function / homology | ![]() intramolecular transferase activity / D-ribose pyranase / D-ribose pyranase activity / intramolecular lyase activity / D-ribose catabolic process / monosaccharide binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Kim, M.-S. / Oh, B.-H. | |||||||||
![]() | ![]() Title: Crystal Structures of Rbsd Leading to the Identification of Cytoplasmic Sugar-Binding Proteins with a Novel Folding Architecture Authors: Kim, M.-S. / Shin, J. / Lee, W. / Lee, H.-S. / Oh, B.-H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.7 KB | Display | ![]() |
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PDB format | ![]() | 109 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402 KB | Display | ![]() |
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Full document | ![]() | 410.1 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14244.438 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Sugar | ChemComp-RP5 / #4: Water | ChemComp-HOH / | Compound details | RBSD IS INVOLVED IN THE HIGH-AFFINITY RIBOSE MEMBRANE TRANSPORT SYSTEM. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.99 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 48339 / % possible obs: 90.3 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % |
Reflection | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 30 Å / Num. measured all: 236173 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 80.7 % / Rmerge(I) obs: 0.225 |
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Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 2.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |