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Yorodumi- PDB-5ey6: CRYSTAL STRUCTURE OF GLUTATHIONE TRANSFERASE F2 FROM POPULUS TRIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ey6 | |||||||||
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Title | CRYSTAL STRUCTURE OF GLUTATHIONE TRANSFERASE F2 FROM POPULUS TRICHOCARPA | |||||||||
Components | Phi class glutathione transferase GSTF2 | |||||||||
Keywords | TRANSFERASE / glutathione / ligandin | |||||||||
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: 1.9 Å | |||||||||
Authors | Didierjean, C. / Rouhier, N. / Pegeot, H. / Gense, F. | |||||||||
Funding support | France, 1items
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Citation | Journal: FEBS J. / Year: 2017 Title: Structural plasticity among glutathione transferase Phi members: natural combination of catalytic residues confers dual biochemical activities. Authors: Pegeot, H. / Mathiot, S. / Perrot, T. / Gense, F. / Hecker, A. / Didierjean, C. / Rouhier, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ey6.cif.gz | 178.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ey6.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ey6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ey6_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 5ey6_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 5ey6_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 5ey6_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/5ey6 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/5ey6 | HTTPS FTP |
-Related structure data
Related structure data | 5f05C 5f06C 5f07C 4ri6S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24517.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_0002s01660g / Production host: Escherichia coli (E. coli) / References: UniProt: B9GQ64, glutathione transferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.5 / Details: 30% PEG MME 2000, 0.1 M Na acetate, Na MES pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.997967 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997967 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.72 Å / Num. obs: 38738 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RI6 Resolution: 1.9→41.658 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→41.658 Å
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Refine LS restraints |
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LS refinement shell |
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