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Yorodumi- PDB-7e9s: Archaeal oligosaccharyltransferase AglB from Archaeoglobus fulgid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e9s | |||||||||
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Title | Archaeal oligosaccharyltransferase AglB from Archaeoglobus fulgidus in complex with an inhibitory peptide and a dolichol-phosphate | |||||||||
Components |
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Keywords | TRANSFERASE / protein n-glycosylation / ternary complex / sequon-containing peptide / dolichol-phosphate | |||||||||
Function / homology | Function and homology information dolichyl-phosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / protein glycosylation / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Taguchi, Y. / Hirata, K. / Kohda, D. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Commun Biol / Year: 2021 Title: The structure of an archaeal oligosaccharyltransferase provides insight into the strict exclusion of proline from the N-glycosylation sequon. Authors: Taguchi, Y. / Yamasaki, T. / Ishikawa, M. / Kawasaki, Y. / Yukimura, R. / Mitani, M. / Hirata, K. / Kohda, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e9s.cif.gz | 439 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e9s.ent.gz | 298.3 KB | Display | PDB format |
PDBx/mmJSON format | 7e9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/7e9s ftp://data.pdbj.org/pub/pdb/validation_reports/e9/7e9s | HTTPS FTP |
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-Related structure data
Related structure data | 5gmyS S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 99159.875 Da / Num. of mol.: 1 / Mutation: G617C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Strain: DSM 4304 / Gene: aglB3, AF_0380 / Plasmid: pET-52b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 References: UniProt: O29867, dolichyl-phosphooligosaccharide-protein glycotransferase |
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#2: Protein/peptide | Mass: 1068.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 27 molecules
#3: Chemical | ChemComp-MN / | ||||
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#4: Chemical | ChemComp-J06 / [( | ||||
#5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-7E8 / ( #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Nonpolymer details | We used TMR(CARBOXYTETRAMETHYLRHODAMINE) to stand for tetramethylrhodamine (RHO), which is a ...We used TMR(CARBOXYTET |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % Description: The microcrystals were needle-shaped with a length greater than 100 micro m and a width/thickness less than 5 micro m. |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 50 mM NaCl, 0.1 M Na-citrate, pH 6.0, 18-22 % PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo N2 stream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 20, 2019 Details: micro-focused beam of 10 micro m x 15 micro m (horizontal x vertical) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.4 Å / Num. obs: 30677 / % possible obs: 100 % / Redundancy: 79.5 % / Biso Wilson estimate: 70.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.432 / Rrim(I) all: 0.435 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 76.9 % / Rmerge(I) obs: 8.718 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3054 / CC1/2: 0.756 / Rrim(I) all: 8.776 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GMY Resolution: 2.7→24.84 Å / SU ML: 0.3262 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7132 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→24.84 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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