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Yorodumi- PDB-5g5a: Glutathione transferase U25 from Arabidopsis thaliana in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g5a | ||||||
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Title | Glutathione transferase U25 from Arabidopsis thaliana in complex with glutathione disulfide | ||||||
Components | GLUTATHIONE S-TRANSFERASE U25 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE / ARABIDOPSIS / TNT | ||||||
Function / homology | Function and homology information 2,4,6-trinitrotoluene catabolic process / toxin catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ahmad, L. / Rylott, E. / Bruce, N.C. / Grogan, G. | ||||||
Citation | Journal: To be Published Title: Structure of Glutathione Transferase U25 from Arabidopsis Thaliana Authors: Ahmad, L. / Rylott, E. / Bruce, N.C. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g5a.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g5a.ent.gz | 161.8 KB | Display | PDB format |
PDBx/mmJSON format | 5g5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5a ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5a | HTTPS FTP |
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-Related structure data
Related structure data | 4topS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 25623.514 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: Q9SHH7, glutathione transferase #2: Chemical | ChemComp-GSH / #3: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.2 M AMMONIUM ACETATE, 0.1 M BIS-TRIS PROPANE PH 5.5 AND 23 % (W/V) PEG 3350; 2 MM GSH |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.54 Å / Num. obs: 75638 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4TOP Resolution: 1.95→48.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.465 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.894 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.54 Å
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Refine LS restraints |
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