+Open data
-Basic information
Entry | Database: PDB / ID: 8p0o | ||||||
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Title | Crystal structure of AaNGT complexed to UDP-Gal | ||||||
Components | Adhesin | ||||||
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 / GALACTOSE-URIDINE-5'-DIPHOSPHATE / Adhesin Function and homology information | ||||||
Biological species | Aggregatibacter aphrophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Pinello, B. / Macias-Leon, J. / Rovira, C. / Hurtado-Guerrero, R. | ||||||
Funding support | Spain, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p0o.cif.gz | 522 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p0o.ent.gz | 423.6 KB | Display | PDB format |
PDBx/mmJSON format | 8p0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p0o_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8p0o_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8p0o_validation.xml.gz | 53.8 KB | Display | |
Data in CIF | 8p0o_validation.cif.gz | 77.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/8p0o ftp://data.pdbj.org/pub/pdb/validation_reports/p0/8p0o | HTTPS FTP |
-Related structure data
Related structure data | 8p0pC 8p0qC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 70866.727 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: Chemical | ChemComp-EDO / #3: Chemical | #4: 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: 2.46 Å3/Da / Density % sol: 50.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: magnesium chloride, HEPES, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→20 Å / Num. obs: 139852 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.76→1.86 Å / Rmerge(I) obs: 1.796 / Num. unique obs: 20146 / CC1/2: 0.43 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.923 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 37.743 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→20 Å
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Refine LS restraints |
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