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Yorodumi- PDB-1m9b: Crystal structure of the 26 kDa glutathione S-transferase from Sc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m9b | ||||||
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Title | Crystal structure of the 26 kDa glutathione S-transferase from Schistosoma japonicum complexed with gamma-glutamyl[S-(2-iodobenzyl)cysteinyl]glycine | ||||||
Components | Glutathione S-Transferase 26 kDa | ||||||
Keywords | TRANSFERASE / Glutathione Transferase / antigen / multigene family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Schistosoma japonicum (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Cardoso, R.M.F. / Daniels, D.S. / Bruns, C.M. / Tainer, J.A. | ||||||
Citation | Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2003 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: Journal: J.Mol.Biol. / Year: 1995 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: Journal: Protein Sci. / Year: 1994 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m9b.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m9b.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/1m9b ftp://data.pdbj.org/pub/pdb/validation_reports/m9/1m9b | HTTPS FTP |
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-Related structure data
Related structure data | 1m99C 1m9aC 1gtaS S: Starting model for refinement C: citing same article (ref.) |
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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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Components on special symmetry positions |
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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.) Schistosoma japonicum (invertebrata) / Plasmid: pGEX-3X / Production host: Escherichia coli (E. coli) / References: UniProt: P08515, glutathione transferase |
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#2: Chemical | ChemComp-IBG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.31 % | ||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.62 Å2 / ksol: 0.367458 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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