+Open data
-Basic information
Entry | Database: PDB / ID: 6lg0 | ||||||
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Title | Crystal structure of SbCGTa in complex with UDP | ||||||
Components | SbCGTa | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | URIDINE-5'-DIPHOSPHATE Function and homology information | ||||||
Biological species | Scutellaria baicalensis (Baikal skullcap) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å | ||||||
Authors | Gao, H.M. / Yun, C.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Dissection of the general two-step di- C -glycosylation pathway for the biosynthesis of (iso)schaftosides in higher plants. Authors: Wang, Z.L. / Gao, H.M. / Wang, S. / Zhang, M. / Chen, K. / Zhang, Y.Q. / Wang, H.D. / Han, B.Y. / Xu, L.L. / Song, T.Q. / Yun, C.H. / Qiao, X. / Ye, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lg0.cif.gz | 489 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lg0.ent.gz | 393 KB | Display | PDB format |
PDBx/mmJSON format | 6lg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/6lg0 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/6lg0 | HTTPS FTP |
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-Related structure data
Related structure data | 6lf6C 6lfnC 6lfzSC 6lg1C 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: 50500.926 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scutellaria baicalensis (Baikal skullcap) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | ChemComp-UDP / #3: Water | ChemComp-HOH / | 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: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium citrate tribasic pH7.0 20%(w/v) Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97851 Å / Relative weight: 1 |
Reflection | Resolution: 2.998→46.958 Å / Num. obs: 59473 / % possible obs: 97.61 % / Redundancy: 6 % / Biso Wilson estimate: 57.33 Å2 / Rpim(I) all: 0.095 / Net I/σ(I): 7.65 |
Reflection shell | Resolution: 3→3.23 Å / Num. unique obs: 11419 / Rpim(I) all: 0.689 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LFZ Resolution: 2.998→46.958 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.15 / Stereochemistry target values: ML
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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 max: 129.74 Å2 / Biso mean: 48.1958 Å2 / Biso min: 11.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.998→46.958 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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