+Open data
-Basic information
Entry | Database: PDB / ID: 1ogd | ||||||
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Title | The Structure of Bacillus subtilis RbsD complexed with D-ribose | ||||||
Components | HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD | ||||||
Keywords | TRANSPORT / RIBOSE / SUGAR TRANSPORT | ||||||
Function / homology | Function and homology information 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 | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / DIRECT METHODS / Resolution: 1.95 Å | ||||||
Authors | Kim, M.-S. / Oh, B.-H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ogd.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogd.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ogd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ogd_validation.pdf.gz | 404.3 KB | Display | wwPDB validaton report |
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Full document | 1ogd_full_validation.pdf.gz | 409.9 KB | Display | |
Data in XML | 1ogd_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1ogd_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogd ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14244.438 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: D-RIBOSE / Source: (natural) BACILLUS SUBTILIS (bacteria) / References: UniProt: P36946 #2: Chemical | #3: Sugar | ChemComp-RIP / #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: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.85 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 62406 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % |
Reflection | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. measured all: 295120 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 92.8 % / Rmerge(I) obs: 0.362 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |