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- PDB-7ec3: Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ec3 | ||||||||||||
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Title | Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide) | ||||||||||||
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![]() | TRANSFERASE / Glycosylation | ||||||||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / cytoplasm / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase, group 1 family protein![]() | ||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||||||||
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 | ![]() | 221.5 KB | Display | ![]() |
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PDB format | ![]() | 175.1 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 ![]() 7ec6C ![]() 7ec7C ![]() 7vfkC ![]() 7vflC ![]() 7vfmC ![]() 7vfnC ![]() 7vfoC 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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Unit cell |
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Components
#1: Protein | Mass: 59631.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: USA300 / Gene: SAUSA300_0550 / Production host: ![]() ![]() #2: Protein/peptide | Mass: 826.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.28 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop Details: 20 mM CaCl2, 85 mM tri-sodium citrate at pH 5.6, 25.5% (w/v) PEG 4,000, and 15% (w/v) glycerol for the SdgB crystal soaked with the 2.66 mM 9mer SD-repeat peptide and 9.60 mM UDP-GlcNAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 60708 / % possible obs: 96.7 % / Redundancy: 5.4 % / CC1/2: 0.934 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 2941 / CC1/2: 0.776 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EC1 Resolution: 2.5→47.05 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.08 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.14 Å2 / Biso mean: 38.96 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 2.5→47.05 Å
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Refine LS restraints |
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