+Open data
-Basic information
Entry | Database: PDB / ID: 7ec6 | ||||||||||||
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Title | Crystal structure of SdgB (complexed with peptides) | ||||||||||||
Components |
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Keywords | TRANSFERASE / Glycosylation | ||||||||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / cytoplasm / Glycosyl transferase, group 1 family protein Function and homology information | ||||||||||||
Biological species | Staphylococcus aureus subsp. aureus USA300 (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Kim, D.-G. / Baek, I. / Lee, Y. / Kim, H.S. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ec6.cif.gz | 216.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ec6.ent.gz | 171.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ec6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/7ec6 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/7ec6 | HTTPS FTP |
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-Related structure data
Related structure data | 7ec1SC 7ec3C 7ec7C 7vfkC 7vflC 7vfmC 7vfnC 7vfoC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 59647.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria) Strain: USA300 / Gene: SAUSA300_0550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2XGN0 #2: Protein/peptide | | Mass: 335.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop Details: 0.2 M MgCl2, 0.1 M Tris-HCl (pH 8.5), and 25% (w/v) polyethylene glycol (PEG) 3,350 incubated with the 2.45 mM 3-mer SD-repeat peptide and 6.14 mM UDP-GlcNAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 87189 / % possible obs: 99.3 % / Redundancy: 4.1 % / CC1/2: 0.992 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 4385 / CC1/2: 0.776 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EC1 Resolution: 1.9→29.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.407 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.162 / 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: 116.48 Å2 / Biso mean: 38.075 Å2 / Biso min: 15.07 Å2
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Refinement step | Cycle: final / Resolution: 1.9→29.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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