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Yorodumi- PDB-7zvp: Crystal structure of poplar glutathione transferase U19 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zvp | ||||||
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Title | Crystal structure of poplar glutathione transferase U19 in complex with glutathione | ||||||
Components | Glutathione transferase | ||||||
Keywords | TRANSFERASE / Glutathione / Tau | ||||||
Function / homology | Function and homology information response to chemical / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Populus trichocarpa (black cottonwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Didierjean, C. / Favier, F. | ||||||
Funding support | France, 1items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Biochemical and Structural Insights on the Poplar Tau Glutathione Transferase GSTU19 and 20 Paralogs Binding Flavonoids. Authors: Sylvestre-Gonon, E. / Morette, L. / Viloria, M. / Mathiot, S. / Boutilliat, A. / Favier, F. / Rouhier, N. / Didierjean, C. / Hecker, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zvp.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zvp.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 7zvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zvp_validation.pdf.gz | 783.5 KB | Display | wwPDB validaton report |
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Full document | 7zvp_full_validation.pdf.gz | 785.1 KB | Display | |
Data in XML | 7zvp_validation.xml.gz | 13 KB | Display | |
Data in CIF | 7zvp_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/7zvp ftp://data.pdbj.org/pub/pdb/validation_reports/zv/7zvp | HTTPS FTP |
-Related structure data
Related structure data | 7zs3SC 7zznC 8a08C 8a0iC 8a0oC 8a0pC 8a0qC 8a0rC S: Starting model for refinement C: citing same article (ref.) |
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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: 25053.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_008G174900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9HKX9, glutathione transferase | ||||
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#2: Chemical | ChemComp-GS8 / | ||||
#3: Chemical | #4: 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: 2.92 Å3/Da / Density % sol: 57.91 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.5 Details: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate pH 6.5 and 18 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→48.1 Å / Num. obs: 39646 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 10 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1927 / CC1/2: 0.94 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZS3 Resolution: 1.61→48.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.103 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.092
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Displacement parameters | Biso mean: 32.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→48.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.62 Å
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