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Yorodumi- PDB-6gsx: FIRST-SPHERE AND SECOND-SPHERE ELECTROSTATIC EFFECTS IN THE ACTIV... -
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-Basic information
Entry | Database: PDB / ID: 6gsx | ||||||
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Title | FIRST-SPHERE AND SECOND-SPHERE ELECTROSTATIC EFFECTS IN THE ACTIVE SITE OF A CLASS MU GLUTATHIONE TRANSFERASE | ||||||
Components | MU CLASS GLUTATHIONE S-TRANSFERASE OF ISOENZYME 3-3 | ||||||
Keywords | TRANSFERASE / GLUTATHIONE TRANSFERASE / ISOENZYME 3-3 / Y6F MUTANT | ||||||
Function / homology | Function and homology information Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase / glutathione transferase activity ...Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase / glutathione transferase activity / response to axon injury / response to amino acid / xenobiotic catabolic process / hepoxilin biosynthetic process / steroid binding / glutathione metabolic process / response to lead ion / cellular response to xenobiotic stimulus / sensory perception of smell / response to ethanol / response to xenobiotic stimulus / protein kinase binding / enzyme binding / protein homodimerization activity / protein-containing complex / extracellular region / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus rattus (black rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.91 Å | ||||||
Authors | Xiao, G. / Ji, X. / Armstrong, R.N. / Gilliland, G.L. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: First-sphere and second-sphere electrostatic effects in the active site of a class mu gluthathione transferase. Authors: Xiao, G. / Liu, S. / Ji, X. / Johnson, W.W. / Chen, J. / Parsons, J.F. / Stevens, W.J. / Gilliland, G.L. / Armstrong, R.N. #1: Journal: Biochemistry / Year: 1994 Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9- ...Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferase as Revealed by X-Ray Crystallographic Analysis of Product Complexes with the Diastereomers of 9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene Authors: Ji, X. / Johnson, W.W. / Sesay, M.A. / Dickert, L. / Prasad, S.M. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L. #2: Journal: J.Am.Chem.Soc. / Year: 1993 Title: Second-Sphere Electrostatic Effects in the Active Site of Glutathione S-Transferase. Observation of an on-Facet Hydrogen Bond between the Side Chain of Threonine 13 and the Pi-Cloud of ...Title: Second-Sphere Electrostatic Effects in the Active Site of Glutathione S-Transferase. Observation of an on-Facet Hydrogen Bond between the Side Chain of Threonine 13 and the Pi-Cloud of Tyrosine 6 and its Influence on Catalysis Authors: Liu, S. / Ji, X. / Gilliland, G.L. / Stevens, W.J. / Armstrong, R.N. #3: Journal: Biochemistry / Year: 1993 Title: Snapshots Along the Reaction Coordinate of an Snar Reaction Catalyzed by Glutathione Transferase Authors: Ji, X. / Armstrong, R.N. / Gilliland, G.L. #4: Journal: J.Biol.Chem. / Year: 1992 Title: Contribution of Tyrosine 6 to the Catalytic Mechanism of Isoenzyme 3-3 of Glutathione S-Transferase Authors: Liu, S. / Zhang, P. / Ji, X. / Johnson, W.W. / Gilliland, G.L. / Armstrong, R.N. #5: Journal: Biochemistry / Year: 1992 Title: The Three-Dimensional Structure of a Glutathione S-Transferase from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2-A Resolution Authors: Ji, X. / Zhang, P. / Armstrong, R.N. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gsx.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gsx.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 6gsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gsx_validation.pdf.gz | 529.8 KB | Display | wwPDB validaton report |
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Full document | 6gsx_full_validation.pdf.gz | 548.5 KB | Display | |
Data in XML | 6gsx_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6gsx_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/6gsx ftp://data.pdbj.org/pub/pdb/validation_reports/gs/6gsx | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.82065, -0.09781, 0.563), Vector: |
-Components
#1: Protein | Mass: 25802.789 Da / Num. of mol.: 2 / Mutation: Y6F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / Gene: CDNA INSERT OF CLONE PGT33MX / Organ: LIVER / Plasmid: PGT33MXY6F / Gene (production host): CDNA INSERT OF CLONE PGT33MX / Production host: Escherichia coli (E. coli) / Strain (production host): M5219 / References: UniProt: P04905, glutathione transferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 18, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. obs: 36475 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 2.55 % / Rmerge(I) obs: 0.07 |
Reflection | *PLUS Num. obs: 36384 / Num. measured all: 92958 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Resolution: 1.91→6 Å / σ(F): 4
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Displacement parameters | Biso mean: 22.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→6 Å
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Refine LS restraints |
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Software | *PLUS Name: GPRLSA / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.152 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |