+Open data
-Basic information
Entry | Database: PDB / ID: 4ri6 | ||||||
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Title | Crystal structure of poplar glutathione transferase F1 | ||||||
Components | Phi class glutathione transferase GSTF1 | ||||||
Keywords | TRANSFERASE / glutathione transferase fold | ||||||
Function / homology | Function and homology information response to chemical / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Populus tremula x Populus tremuloides (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.523 Å | ||||||
Authors | Pegeot, H. / Koh, C.S. / Didierjean, C. / Rouhier, N. | ||||||
Citation | Journal: Front Plant Sci / Year: 2014 Title: The poplar Phi class glutathione transferase: expression, activity and structure of GSTF1. Authors: Pegeot, H. / Koh, C.S. / Petre, B. / Mathiot, S. / Duplessis, S. / 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 | 4ri6.cif.gz | 276.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ri6.ent.gz | 229.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ri6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/4ri6 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/4ri6 | HTTPS FTP |
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-Related structure data
Related structure data | 4ri7C 1gnwS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 24351.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus tremula x Populus tremuloides (plant) Gene: POPTR_0002s01650g / Production host: Escherichia coli (E. coli) / References: UniProt: A9PHH6, glutathione transferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | AUTHORS HAVE CLARIFIED THAT DISCREPANC | |
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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: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 6.5 Details: 30% w/v PEG4000, 100 mM MES sodium, pH 6.5, MICROBATCH UNDER OIL, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Aug 22, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→18.281 Å / Num. obs: 65579 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.4 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GNW Resolution: 1.523→18.281 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 18.67 / 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: 1.523→18.281 Å
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Refine LS restraints |
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LS refinement shell |
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