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Yorodumi- PDB-1pn9: Crystal structure of an insect delta-class glutathione S-transfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pn9 | ||||||
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Title | Crystal structure of an insect delta-class glutathione S-transferase from a DDT-resistant strain of the malaria vector Anopheles gambiae | ||||||
Components | Glutathione S-transferase 1-6 | ||||||
Keywords | TRANSFERASE / protein inhibitor complex | ||||||
Function / homology | Function and homology information DDT-dehydrochlorinase / DDT-dehydrochlorinase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Anopheles gambiae (African malaria mosquito) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chen, L. / Hall, P.R. / Zhou, X.E. / Ranson, H. / Hemingway, J. / Meehan, E.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of an insect delta-class glutathione S-transferase from a DDT-resistant strain of the malaria vector Anopheles gambiae. Authors: Chen, L. / Hall, P.R. / Zhou, X.E. / Ranson, H. / Hemingway, J. / Meehan, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pn9.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pn9.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/1pn9 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/1pn9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23469.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Gene: GST1-6 / Plasmid: pXaggst1-6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q93113, glutathione transferase #2: Chemical | #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: 2.39 Å3/Da / Density % sol: 48.51 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000, 2-propanol, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 26280 / Num. obs: 26280 / % possible obs: 84.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 7.4 / Num. unique all: 3704 / % possible all: 72.8 |
Reflection | *PLUS Num. measured all: 118522 |
Reflection shell | *PLUS % possible obs: 87.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: dmGST21 Resolution: 2→19.57 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.167 Å2 / ksol: 0.389783 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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