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Yorodumi- PDB-2il3: Structures of an Insect Epsilon-class Glutathione S-transferase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2il3 | ||||||
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Title | Structures of an Insect Epsilon-class Glutathione S-transferase from the Malaria Vector Anopheles Gambiae: Evidence for High DDT-detoxifying Activity | ||||||
Components | Epsilon-class Glutathione S-transferase | ||||||
Keywords | TRANSFERASE / Epsilon-class Glutathione / S-transferase | ||||||
Function / homology | Function and homology information glutathione transferase / glutathione transferase activity / glutathione metabolic process Similarity search - Function | ||||||
Biological species | Anopheles gambiae (African malaria mosquito) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, Y. / Hemingway, J. / Ranson, H. / Meehan, E.J. / Chen, L. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2008 Title: Structure of an insect epsilon class glutathione S-transferase from the malaria vector Anopheles gambiae provides an explanation for the high DDT-detoxifying activity Authors: Wang, Y. / Qiu, L. / Ranson, H. / Lumjuan, N. / Hemingway, J. / Setzer, W.N. / Meehan, E.J. / Chen, L. | ||||||
History |
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Remark 999 | SEQUENCE TWO CLOSEST MATCHES IN SEQUENCE DATABASES, UNP Q7PVS6_ANOGA AND GB EAA43411 HAVE ... SEQUENCE TWO CLOSEST MATCHES IN SEQUENCE DATABASES, UNP Q7PVS6_ANOGA AND GB EAA43411 HAVE CONFLICTS WITH SEQUENCE AS SEEN IN THE ELECTRON DENSITY MAPS: Q7PVS6_ANOGA HAS ADDITIONAL N-TERMINAL LYSINE EAA43411 HAS ADDITIONAL C-TERMINAL LYSINE AND ALANINE (REPORTED HERE AS INSERTIONS) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2il3.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2il3.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 2il3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2il3_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 2il3_full_validation.pdf.gz | 449.5 KB | Display | |
Data in XML | 2il3_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 2il3_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/2il3 ftp://data.pdbj.org/pub/pdb/validation_reports/il/2il3 | HTTPS FTP |
-Related structure data
Related structure data | 2imiC 2imkC 1pn9S 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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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 24879.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Gene: AF316636 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q7PVS6, glutathione transferase #2: 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: 1.99 Å3/Da / Density % sol: 38.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5 and 25% w/v Polyethylene Glycerol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 11, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.9 % / Av σ(I) over netI: 5.4 / Number: 56565 / Rmerge(I) obs: 0.105 / Χ2: 1 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 19304 / % possible obs: 92.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.2→50 Å / Num. all: 19304 / Num. obs: 19304 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 34.206 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Χ2: 1.004 / Net I/σ(I): 5.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1728 / Rsym value: 0.0135 / Χ2: 0.8 / % possible all: 85.2 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 1PN9 Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.08 / SU ML: 0.209 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.43 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.886 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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