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Yorodumi- PDB-8hjf: Crystal structure of glycosyltransferase SgUGT94-289-3 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hjf | |||||||||||||||
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Title | Crystal structure of glycosyltransferase SgUGT94-289-3 in complex with M5, state 2 | |||||||||||||||
Components | glycosyltransferase | |||||||||||||||
Keywords | TRANSFERASE / mogroside / UGT / Siraitia grosvenorii | |||||||||||||||
Function / homology | : / Chem-POG / URIDINE-5'-DIPHOSPHATE Function and homology information | |||||||||||||||
Biological species | Siraitia grosvenorii (arhat fruit) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||||||||
Authors | Li, M. / Zhang, S. / Cui, S. | |||||||||||||||
Funding support | China, United Kingdom, 4items
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Citation | Journal: To Be Published Title: Structural insights into the catalytic selectivity of SgUGT94-289-3 towards mogropides Authors: Cui, S. / Zhang, S. / Wang, N. / Luo, Z. / Su, X. / Ma, X. / Li, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hjf.cif.gz | 212.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hjf.ent.gz | 164.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hjf_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8hjf_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8hjf_validation.xml.gz | 45 KB | Display | |
Data in CIF | 8hjf_validation.cif.gz | 62.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/8hjf ftp://data.pdbj.org/pub/pdb/validation_reports/hj/8hjf | HTTPS FTP |
-Related structure data
Related structure data | 6jtdS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 51622.820 Da / Num. of mol.: 2 / Mutation: G152A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Siraitia grosvenorii (arhat fruit) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 640 molecules
#2: Chemical | Mass: 1287.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C60H102O29 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.37 Å3/Da / Density % sol: 48.13 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: Tris-HCl, polyethylene glycol 3350, NaCl, Polypropylene glycol P400. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.66 Å / Num. obs: 64729 / % possible obs: 99.62 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.88 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2→2.071 Å / Num. unique obs: 6412 / CC1/2: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JTD Resolution: 2→19.66 Å / SU ML: 0.2737 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3166 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 27.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.66 Å
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Refine LS restraints |
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LS refinement shell |
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