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Yorodumi- PDB-5j4u: Crystal structure of a glutathione S-transferase PtGSTU30 from Po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j4u | ||||||
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Title | Crystal structure of a glutathione S-transferase PtGSTU30 from Populus trichocarpa in complex with GSH | ||||||
Components | Glutathione transferase family protein | ||||||
Keywords | TRANSFERASE / GST / Complex / GSH | ||||||
Function / homology | Function and homology information response to chemical / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Populus trichocarpa (black cottonwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.249 Å | ||||||
Authors | Yang, Q. / Gu, J. / Yang, M. / Zeng, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Functional and Structural Profiles of GST Gene Family from Three Populus Species Revealed the Sequence-function Decoupling of Orthologous Genes Authors: Yang, Q. / Han, X. / Gu, J. / Liu, Y. / Yang, M. / Zeng, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j4u.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j4u.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 5j4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j4u_validation.pdf.gz | 721 KB | Display | wwPDB validaton report |
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Full document | 5j4u_full_validation.pdf.gz | 722 KB | Display | |
Data in XML | 5j4u_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 5j4u_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/5j4u ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4u | HTTPS FTP |
-Related structure data
Related structure data | 5j5nC 4topS 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: 26848.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_0011s14410g / Plasmid: pET30 / Details (production host): modified pET30a vector / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: B9I0G5 |
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#2: Chemical | ChemComp-GSH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.74 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 1.8M Ammonium sulfate, 0.1M Sodium citrate tribasic dehydrate, pH 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.249→40.85 Å / Num. obs: 68741 / % possible obs: 98.5 % / Redundancy: 7.2 % / Net I/σ(I): 45.91 |
Reflection shell | Resolution: 1.25→1.27 Å |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TOP Resolution: 1.249→40.85 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.34 Å2 / Biso mean: 16.4673 Å2 / Biso min: 7.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.249→40.85 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: 25
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