+Open data
-Basic information
Entry | Database: PDB / ID: 8p0q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of AaNGT complexed to UDP and a peptide | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / N-glycosylation / Asn tautomeric form / AAD / Glycosyltransferase / GT-B | ||||||
Function / homology | HMW1 domain 2 / HMW1C N-terminal / HMW1C N-terminal / HMW1 domain 2 / glycosyltransferase activity / URIDINE-5'-DIPHOSPHATE / Adhesin Function and homology information | ||||||
Biological species | Aggregatibacter aphrophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Piniello, B. / Macias-Leon, J. / Rovira, C. / Hurtado-Guerrero, R. | ||||||
Funding support | Spain, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Molecular basis for bacterial N-glycosylation by a soluble HMW1C-like N-glycosyltransferase. Authors: Piniello, B. / Macias-Leon, J. / Miyazaki, S. / Garcia-Garcia, A. / Companon, I. / Ghirardello, M. / Taleb, V. / Veloz, B. / Corzana, F. / Miyagawa, A. / Rovira, C. / Hurtado-Guerrero, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8p0q.cif.gz | 504.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8p0q.ent.gz | 416.3 KB | Display | PDB format |
PDBx/mmJSON format | 8p0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/8p0q ftp://data.pdbj.org/pub/pdb/validation_reports/p0/8p0q | HTTPS FTP |
---|
-Related structure data
Related structure data | 8p0oC 8p0pC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 616 / Label seq-ID: 1 - 616
|
-Components
#1: Protein | Mass: 70809.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aggregatibacter aphrophilus (bacteria) / Gene: DOL88_00785 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3M6PNT1 #2: Protein/peptide | Mass: 724.761 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: It is a peptide / Source: (synth.) Aggregatibacter aphrophilus (bacteria) #3: Chemical | #4: 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: 2.35 Å3/Da / Density % sol: 47.74 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: polyacrylic acid 5,100 sodium salt, HEPES sodium salt |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 34243 / % possible obs: 99.7 % / Redundancy: 8.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.177 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Num. unique obs: 4940 / CC1/2: 0.352 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / SU B: 37.268 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 81.251 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→19.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|