+Open data
-Basic information
Entry | Database: PDB / ID: 7ec7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of SdgB (complexed with phosphate ions) | ||||||||||||
Components | Glycosyl transferase, group 1 family proteinGlycosyltransferase | ||||||||||||
Keywords | TRANSFERASE / Glycosylation | ||||||||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / PHOSPHATE ION / Glycosyl transferase, group 1 family protein Function and homology information | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Kim, D.-G. / Baek, I. / Lee, Y. / Kim, H.S. | ||||||||||||
Funding support | Korea, Republic Of, 3items
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ec7.cif.gz | 213.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ec7.ent.gz | 172 KB | Display | PDB format |
PDBx/mmJSON format | 7ec7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/7ec7 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/7ec7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7ec1SC 7ec3C 7ec6C 7vfkC 7vflC 7vfmC 7vfnC 7vfoC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59888.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria) Strain: USA300 / Gene: SAUSA300_0550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2XGN0 #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.78 % |
---|---|
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: 287 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EC1 Resolution: 3.2→29.98 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.873 / SU B: 18.958 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 134.13 Å2 / Biso mean: 60.717 Å2 / Biso min: 18.52 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→29.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|