+Open data
-Basic information
Entry | Database: PDB / ID: 6jel | ||||||
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Title | Structure of Phytolacca americana apo UGT2 | ||||||
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: 2.3 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 | 6jel.cif.gz | 186.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jel.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 6jel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jel_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 6jel_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 6jel_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 6jel_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/6jel ftp://data.pdbj.org/pub/pdb/validation_reports/je/6jel | HTTPS FTP |
-Related structure data
Related structure data | 6jemC 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 5 - 466 / Label seq-ID: 25 - 486
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-Components
#1: Protein | Mass: 53829.195 Da / Num. of mol.: 2 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) star References: UniProt: B5MGN7, Transferases; Glycosyltransferases; Hexosyltransferases #2: Water | ChemComp-HOH / | 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: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M magnesium formate 0.1 M MOPS pH 7.0 17% w/v PEG 3350 |
-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: Oct 8, 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: 2.3→50 Å / Num. obs: 45171 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2216 / CC1/2: 0.757 / Rrim(I) all: 1.03 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VCH Resolution: 2.3→36.64 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.24
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.154 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→36.64 Å
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Refine LS restraints |
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