+Open data
-Basic information
Entry | Database: PDB / ID: 7erx | ||||||
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Title | Glycosyltransferase in complex with UDP and STB | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase in steviol glucosylation | ||||||
Function / homology | Function and homology information UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Zhu, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Catalytic flexibility of rice glycosyltransferase OsUGT91C1 for the production of palatable steviol glycosides. Authors: Zhang, J. / Tang, M. / Chen, Y. / Ke, D. / Zhou, J. / Xu, X. / Yang, W. / He, J. / Dong, H. / Wei, Y. / Naismith, J.H. / Lin, Y. / Zhu, X. / Cheng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7erx.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7erx.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 7erx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7erx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7erx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7erx_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 7erx_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/7erx ftp://data.pdbj.org/pub/pdb/validation_reports/er/7erx | HTTPS FTP |
-Related structure data
Related structure data | 7erySC 7es0C 7es1C 7es2C S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 51042.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: Os03g0702000, OSNPB_030702000 / Production host: Escherichia coli (E. coli) References: UniProt: Q0DPB7, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-UDP / |
#4: Chemical | ChemComp-JC6 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES-NaOH buffer pH 6.5 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: BL18U1 / Wavelength: 0.97915 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.92→109.39 Å / Num. obs: 38620 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.036 / Rrim(I) all: 0.066 / Net I/σ(I): 14.5 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ERY Resolution: 1.92→66.297 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 9.875 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.125 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.917 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→66.297 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: -8.3427 Å / Origin y: -9.2761 Å / Origin z: 20.2902 Å
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Refinement TLS group | Selection: ALL |