+Open data
-Basic information
Entry | Database: PDB / ID: 6inh | |||||||||
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Title | A glycosyltransferase with UDP and the substrate | |||||||||
Components | UDP-glycosyltransferase 76G1 | |||||||||
Keywords | TRANSFERASE / complex | |||||||||
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: 2.1 Å | |||||||||
Authors | Zhu, X. | |||||||||
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 | 6inh.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6inh.ent.gz | 162.3 KB | Display | PDB format |
PDBx/mmJSON format | 6inh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6inh_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6inh_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6inh_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 6inh_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/6inh ftp://data.pdbj.org/pub/pdb/validation_reports/in/6inh | HTTPS FTP |
-Related structure data
Related structure data | 6infC 6ingC 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: 53158.227 Da / Num. of mol.: 1 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: Chemical | #5: 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: 2.35 Å3/Da / Density % sol: 47.56 % |
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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: 2.1→84.46 Å / Num. obs: 29548 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.091 / Rrim(I) all: 0.158 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 2159 / CC1/2: 0.916 / Rpim(I) all: 0.212 / Rrim(I) all: 0.361 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PQ6 Resolution: 2.1→61.84 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.853 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.764 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→61.84 Å
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Refine LS restraints |
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