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Open data
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Basic information
Entry | Database: PDB / ID: 7vfo | ||||||||||||
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Title | Crystal structure of SdgB (Phosphate-binding form) | ||||||||||||
![]() | Glycosyl transferase, group 1 family protein | ||||||||||||
![]() | TRANSFERASE / Glycosylation | ||||||||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / cytoplasm / PHOSPHATE ION / Glycosyl transferase, group 1 family protein![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kim, D.-G. / Baek, I. / Lee, Y. / Kim, H.S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins. Authors: Kim, D.G. / Baek, I. / Lee, Y. / Kim, H. / Kim, J.Y. / Bang, G. / Kim, S. / Yoon, H.J. / Han, B.W. / Suh, S.W. / Kim, H.S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.8 KB | Display | ![]() |
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PDB format | ![]() | 171.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ec1SC ![]() 7ec3C ![]() 7ec6C ![]() 7ec7C ![]() 7vfkC ![]() 7vflC ![]() 7vfmC ![]() 7vfnC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 59888.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: USA300 / Gene: SAUSA300_0550 / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.6 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop Details: 1.2 M NaH2PO4, 0.8 M K2HPO4, and 0.1 M CAPS-NaOH (pH 10.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 26949 / % possible obs: 89 % / Redundancy: 8.2 % / CC1/2: 0.973 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 3.2→3.26 Å / Num. unique obs: 1492 / CC1/2: 0.916 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EC1 Resolution: 3.2→29.98 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.7 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.2 Å2 / Biso mean: 55.4195 Å2 / Biso min: 24.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→29.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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