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Yorodumi- PDB-8agq: Crystal structure of anthocyanin-related GSTF8 from Populus trich... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8agq | ||||||
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Title | Crystal structure of anthocyanin-related GSTF8 from Populus trichocarpa in complex with (-)-catechin and glutathione | ||||||
Components | Glutathione transferase | ||||||
Keywords | TRANSFERASE / Anthocyanin / Dehydratase | ||||||
Function / homology | Function and homology information glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / response to toxic substance / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Populus trichocarpa (black cottonwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.093 Å | ||||||
Authors | Eichenberger, M. / Hueppi, S. / Schwander, T. / Mittl, P. / Buller, M.R. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nat Catal / Year: 2023 Title: The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis. Authors: Eichenberger, M. / Schwander, T. / Huppi, S. / Kreuzer, J. / Mittl, P.R.E. / Peccati, F. / Jimenez-Oses, G. / Naesby, M. / Buller, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8agq.cif.gz | 204.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8agq.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 8agq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8agq_validation.pdf.gz | 995.6 KB | Display | wwPDB validaton report |
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Full document | 8agq_full_validation.pdf.gz | 995.7 KB | Display | |
Data in XML | 8agq_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 8agq_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8agq ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agq | HTTPS FTP |
-Related structure data
Related structure data | 5f07S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24458.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_017G138800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9MWW0, glutathione transferase | ||||
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#2: Chemical | ChemComp-GSH / | ||||
#3: Chemical | ChemComp-M5O / ( | ||||
#4: Chemical | ChemComp-NA / #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: 2.56 Å3/Da / Density % sol: 51.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 1 part protein solution (30mM Tris pH 8, 200mM NaCl, 1mM EDTA) 1 part buffer (100mM MES pH 6.4, 200mM MgCl2, 17.9% PEG200) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999995 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999995 Å / Relative weight: 1 |
Reflection | Resolution: 1.093→38.496 Å / Num. obs: 101092 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.093→1.11 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5007 / CC1/2: 0.817 / Rrim(I) all: 0.667 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F07 Resolution: 1.093→38.496 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.143 / WRfactor Rwork: 0.124 / SU B: 0.888 / SU ML: 0.018 / Average fsc free: 0.977 / Average fsc work: 0.9799 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.026 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: 14.844 Å2
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Refinement step | Cycle: LAST / Resolution: 1.093→38.496 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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