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Yorodumi- PDB-6jem: Structure of Phytolacca americana UGT2 complexed with UDP-2fluoro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jem | ||||||
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Title | Structure of Phytolacca americana UGT2 complexed with UDP-2fluoro-glucose and resveratrol | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase | ||||||
Function / homology | Function and homology information UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases Similarity search - Function | ||||||
Biological species | Phytolacca americana (American pokeweed) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Maharjan, R. / Fukuda, Y. / Nakayama, T. / Hamada, H. / Ozaki, S. / Inoue, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochemistry / Year: 2020 Title: An Ambidextrous Polyphenol GlycosyltransferasePaGT2 fromPhytolacca americana. Authors: Maharjan, R. / Fukuda, Y. / Shimomura, N. / Nakayama, T. / Okimoto, Y. / Kawakami, K. / Nakayama, T. / Hamada, H. / Inoue, T. / Ozaki, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jem.cif.gz | 266.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jem.ent.gz | 212.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jem_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6jem_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6jem_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 6jem_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/6jem ftp://data.pdbj.org/pub/pdb/validation_reports/je/6jem | HTTPS FTP |
-Related structure data
Related structure data | 6jelC 6jenC 2vchS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 53829.195 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytolacca americana (American pokeweed) Gene: PaGT2 / Plasmid: pCold / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): star References: UniProt: B5MGN7, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | #3: Chemical | Has ligand of interest | N | Sequence details | The sequence database with ID B5MGN7 contains residue TYR at position 211. However, after observing ...The sequence database with ID B5MGN7 contains residue TYR at position 211. However, after observing the discrepancy, authors confirmed that residue at 211 is ASN and not TYR. The depositers will soon correct the sequence in the database. | |
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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: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.11 M potassium citrate 0.06 M lithium citrate 0.11 M sodium phosphate 23% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 51665 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.04 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2535 / CC1/2: 0.689 / Rrim(I) all: 0.514 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VCH Resolution: 2.6→44.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.578 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.087 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→44.85 Å
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Refine LS restraints |
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