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Yorodumi- PDB-1pa3: Crystal Structure of Glutathione-S-transferase from Plasmodium fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pa3 | ||||||
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Title | Crystal Structure of Glutathione-S-transferase from Plasmodium falciparum | ||||||
Components | Glutathione s-transferase, putative | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information Heme degradation / Paracetamol ADME / Glutathione conjugation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Detoxification of Reactive Oxygen Species / Azathioprine ADME / Neutrophil degranulation / glutathione transferase / glutathione transferase activity / glutathione metabolic process Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.7 Å | ||||||
Authors | Perbandt, M. / Betzel, C. / Liebau, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Native and inhibited structure of a Mu class-related glutathione S-transferase from Plasmodium falciparum Authors: Perbandt, M. / Burmeister, C. / Walter, R.D. / Betzel, C. / Liebau, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pa3.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pa3.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pa3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/1pa3 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/1pa3 | HTTPS FTP |
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-Related 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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-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) Production host: Escherichia coli (E. coli) / References: UniProt: Q95V54, UniProt: Q8MU52*PLUS #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: 2.08 Å3/Da / Density % sol: 40.85 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ammonium sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop / Details: Burmeister, C., (2003) Acta Cryst., D59, 1469. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 13330 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 2.6 Å / % possible all: 97.92 |
Reflection | *PLUS Num. obs: 13027 / % possible obs: 97.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.13 |
Reflection shell | *PLUS Lowest resolution: 2.69 Å / % possible obs: 94.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.3 |
-Processing
Software | Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||
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Refinement | Method to determine structure: MIR / Resolution: 2.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Num. reflection Rfree: 658 / % reflection Rfree: 5 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.205 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.351 / Rfactor Rwork: 0.322 |