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Yorodumi- PDB-8j30: Crystal structure of ApNGT with Q469A and M218A mutations in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j30 | |||||||||||||||
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Title | Crystal structure of ApNGT with Q469A and M218A mutations in complex with UDP-GLC | |||||||||||||||
Components | UDP-glucose:protein N-beta-glucosyltransferase | |||||||||||||||
Keywords | TRANSFERASE / Actinobacillus pleuropneumoniae / N-glycosyltransferase | |||||||||||||||
Function / homology | Function and homology information Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / protein glycosylation / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Actinobacillus pleuropneumoniae serovar 5b str. L20 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | |||||||||||||||
Authors | Feng, Y. / Hao, Z. / Guo, Q. / Zheng, J. / Da, L. / Peng, W. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Jacs Au / Year: 2023 Title: Investigation of the Catalytic Mechanism of a Soluble N-glycosyltransferase Allows Synthesis of N-glycans at Noncanonical Sequons. Authors: Hao, Z. / Guo, Q. / Feng, Y. / Zhang, Z. / Li, T. / Tian, Z. / Zheng, J. / Da, L.T. / Peng, W. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j30.cif.gz | 464.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j30.ent.gz | 379.8 KB | Display | PDB format |
PDBx/mmJSON format | 8j30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/8j30 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/8j30 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 71532.242 Da / Num. of mol.: 2 / Mutation: Q469A,M218A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinobacillus pleuropneumoniae serovar 5b str. L20 (bacteria) Gene: APL_1635 / Production host: Escherichia coli (E. coli) References: UniProt: A3N2T3, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | ChemComp-UPG / | #3: Chemical | ChemComp-UDP / | 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: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M TBis-Tris-HCl (pH 6.5), 2%(v/v) Tacsimate(pH 6.0), 20%(v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→50 Å / Num. obs: 30111 / % possible obs: 98.78 % / Redundancy: 6.2 % / CC1/2: 0.985 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.88→2.93 Å / Num. unique obs: 28618 / CC1/2: 0.721 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→47.18 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→47.18 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 12.038 Å / Origin y: 24.4499 Å / Origin z: 18.5959 Å
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Refinement TLS group | Selection details: all |