[English] 日本語
![](img/lk-miru.gif)
- PDB-1m9b: Crystal structure of the 26 kDa glutathione S-transferase from Sc... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1m9b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the 26 kDa glutathione S-transferase from Schistosoma japonicum complexed with gamma-glutamyl[S-(2-iodobenzyl)cysteinyl]glycine | ||||||
![]() | Glutathione S-Transferase 26 kDa | ||||||
![]() | TRANSFERASE / Glutathione Transferase / antigen / multigene family | ||||||
Function / homology | ![]() glutathione transferase / glutathione transferase activity / glutathione metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cardoso, R.M.F. / Daniels, D.S. / Bruns, C.M. / Tainer, J.A. | ||||||
![]() | ![]() Title: Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum Authors: Cardoso, R.M.F. / Daniels, D.S. / Bruns, C.M. / Tainer, J.A. #1: ![]() Title: Crystal structures of a schistosomal drug and vaccine target: glutathione S-transferase from Schistosoma japonica and its complex with the leading antischistosomal drug praziquantel Authors: McTigue, M.A. / Williams, D.R. / Tainer, J.A. #2: ![]() Title: Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV Authors: Lim, K. / Ho, J.X. / Keeling, K. / Gilliland, G.L. / Ji, X. / Ruker, F. / Carter, D.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1m99C ![]() 1m9aC ![]() 1gtaS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | There is one GST subunit per asymmetric unit and the second subunit of the GST dimer is generated by the symmetry operation: -x, -x+y, -z |
-
Components
#1: Protein | Mass: 25534.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-IBG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.31 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium sulfate, ethanol, dithiothrietol, threalose, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 1996 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.914 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→99 Å / Num. all: 9743 / Num. obs: 9743 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.078 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 871 / Rsym value: 0.689 / % possible all: 89.4 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 26 Å / Num. measured all: 56234 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 89.4 % / Rmerge(I) obs: 0.689 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1GTA Resolution: 2.6→26 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1537461.75 / Data cutoff high rms absF: 1537461.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.62 Å2 / ksol: 0.367458 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|