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Yorodumi- PDB-6ing: A complex structure of H25A mutant of glycosyltransferase with UDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ing | |||||||||
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Title | A complex structure of H25A mutant of glycosyltransferase with UDP | |||||||||
Components | UDP-glycosyltransferase 76G1 | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases Similarity search - Function | |||||||||
Biological species | Stevia rebaudiana (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å | |||||||||
Authors | Zhu, X. / Naismith, J.H. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: Hydrophobic recognition allows the glycosyltransferase UGT76G1 to catalyze its substrate in two orientations. Authors: Yang, T. / Zhang, J. / Ke, D. / Yang, W. / Tang, M. / Jiang, J. / Cheng, G. / Li, J. / Cheng, W. / Wei, Y. / Li, Q. / Naismith, J.H. / Zhu, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ing.cif.gz | 280.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ing.ent.gz | 228.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ing.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ing_validation.pdf.gz | 799.4 KB | Display | wwPDB validaton report |
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Full document | 6ing_full_validation.pdf.gz | 802.8 KB | Display | |
Data in XML | 6ing_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 6ing_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/6ing ftp://data.pdbj.org/pub/pdb/validation_reports/in/6ing | HTTPS FTP |
-Related structure data
Related structure data | 6infC 6inhC 6iniC 2pq6S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 53091.160 Da / Num. of mol.: 1 / Mutation: H25A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stevia rebaudiana (plant) / Gene: UGT76G1 / Production host: Escherichia coli (E. coli) References: UniProt: Q6VAB4, Transferases; Glycosyltransferases; Hexosyltransferases | ||
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#2: Chemical | ChemComp-UDP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium citrate buffer at pH 5.4 and 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.698→85.689 Å / Num. obs: 55785 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.043 / Rrim(I) all: 0.096 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.7→1.74 Å / Rmerge(I) obs: 3.288 / Num. measured obs: 39564 / Num. unique obs: 4095 / CC1/2: 0.451 / Rpim(I) all: 1.678 / Rrim(I) all: 3.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PQ6 Resolution: 1.698→85.689 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.698→85.689 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 |
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