[English] 日本語
Yorodumi- PDB-1ml6: Crystal Structure of mGSTA2-2 in Complex with the Glutathione Con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ml6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of mGSTA2-2 in Complex with the Glutathione Conjugate of Benzo[a]pyrene-7(R),8(S)-Diol-9(S),10(R)-Epoxide | ||||||
Components | Glutathione S-Transferase GT41A | ||||||
Keywords | TRANSFERASE / GST detoxification / mGSTA2-2 | ||||||
Function / homology | Function and homology information response to stilbenoid / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / xenobiotic metabolic process / response to bacterium / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gu, Y. / Xiao, B. / Wargo, H.L. / Bucher, M.H. / Singh, S.V. / Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Residues 207, 216, and 221 and the catalytic activity of mGSTA1-1 and mGSTA2-2 toward benzo[a]pyrene-(7R,8S)-diol-(9S,10R)-epoxide Authors: Gu, Y. / Xiao, B. / Wargo, H.L. / Bucher, M.H. / Singh, S.V. / Ji, X. #1: Journal: Biochemistry / Year: 2000 Title: Residue R216 and Catalytic Efficiency of a Murine Class Alpha Glutathione S-Transferase toward Benzo[a]pyrene 7(R),8(S)-Diol-9(S),10(R)-Epoxide Authors: Gu, Y. / Singh, S.V. / Ji, X. #2: Journal: Biochemistry / Year: 1999 Title: Amino Acid Substitutions at Positions 207 and 221 Contribute to Catalytic Differences between Murine Glutathione S-Transferase A1-1 and A2-2 toward (+)-anti-7,8-Dihydroxy-9,10-epoxy-7,8,9,10- ...Title: Amino Acid Substitutions at Positions 207 and 221 Contribute to Catalytic Differences between Murine Glutathione S-Transferase A1-1 and A2-2 toward (+)-anti-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene Authors: Xia, H. / Gu, Y. / Pan, S.-S. / Ji, X. / Singh, S.V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ml6.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ml6.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ml6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/1ml6 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/1ml6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1f3aS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 25455.799 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: GST / Plasmid: pET-11d / Production host: Escherichia coli (E. coli) / References: UniProt: P10648, glutathione transferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, isopropanol, NaHepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 1999 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 37794 / Num. obs: 37794 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.038 / Net I/σ(I): 18.68 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.44 / Rsym value: 0.448 / % possible all: 99.2 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Redundancy: 4.59 % |
Reflection shell | *PLUS % possible obs: 99.2 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F3A Resolution: 1.9→26.28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1753798.71 / Data cutoff high rms absF: 1753798.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.9908 Å2 / ksol: 0.335569 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→26.28 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. reflection obs: 35892 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|