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Yorodumi- PDB-3frc: Tetramerization and Cooperativity in Plasmodium falciparum glutat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3frc | ||||||
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Title | Tetramerization and Cooperativity in Plasmodium falciparum glutathione transferase are mediated by the atypic loop 113-118 | ||||||
Components | Glutathione S-transferase | ||||||
Keywords | TRANSFERASE / PfGST / Glutathione S-transferase / Plasmodium falciparum | ||||||
Function / homology | Function and homology information Glutathione conjugation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione transferase / glutathione transferase activity Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Perbandt, M. / Liebau, E. / Ricci, G. | ||||||
Citation | Journal: To be Published Title: Tetramerization and Cooperativity in Plasmodium falciparum glutathione transferase are mediated by the atypic loop 113-118 Authors: Perbandt, M. / Liebau, E. / Ricci, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3frc.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3frc.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 3frc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/3frc ftp://data.pdbj.org/pub/pdb/validation_reports/fr/3frc | HTTPS FTP |
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-Related structure data
Related structure data | 3fr3C 3fr6C 3fr9C 1q4jS 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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Unit cell |
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-Components
#1: Protein | Mass: 24817.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: GST / Plasmid: pJC20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8MU52, glutathione transferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.36 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 34227 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q4J Resolution: 2→19.71 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.569 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.184 / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.018 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.998→2.049 Å / Total num. of bins used: 20
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