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Yorodumi- PDB-4pgt: CRYSTAL STRUCTURE OF HGSTP1-1[V104] COMPLEXED WITH THE GSH CONJUG... -
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-Basic information
Entry | Database: PDB / ID: 4pgt | ||||||
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Title | CRYSTAL STRUCTURE OF HGSTP1-1[V104] COMPLEXED WITH THE GSH CONJUGATE OF (+)-ANTI-BPDE | ||||||
Components | PROTEIN (GLUTATHIONE S-TRANSFERASE) | ||||||
Keywords | TRANSFERASE / PI CLASS / HGSTP1-1[V104] / DETOXIFICATION | ||||||
Function / homology | Function and homology information S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of leukocyte proliferation / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / Paracetamol ADME / JUN kinase binding / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / negative regulation of MAPK cascade / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / glutathione metabolic process / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / response to reactive oxygen species / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / vesicle / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Ji, X. / Blaszczyk, J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structure and function of residue 104 and water molecules in the xenobiotic substrate-binding site in human glutathione S-transferase P1-1. Authors: Ji, X. / Blaszczyk, J. / Xiao, B. / O'Donnell, R. / Hu, X. / Herzog, C. / Singh, S.V. / Zimniak, P. #1: Journal: Biochemistry / Year: 1997 Title: Structure and function of the xenobiotic substrate-binding site and location of a potential non-substrate-binding site in a class pi glutathione S-transferase. Authors: Ji, X. / Tordova, M. / O'Donnell, R. / Parsons, J.F. / Hayden, J.B. / Gilliland, G.L. / Zimniak, P. #2: Journal: Eur.J.Biochem. / Year: 1994 Title: Naturally occurring human glutathione S-transferase GSTP1-1 isoforms with isoleucine and valine in position 104 differ in enzymic properties. Authors: Zimniak, P. / Nanduri, B. / Pikula, S. / Bandorowicz-Pikula, J. / Singhal, S.S. / Srivastava, S.K. / Awasthi, S. / Awasthi, Y.C. #3: Journal: J.Mol.Biol. / Year: 1992 Title: Three-dimensional structure of class pi glutathione S-transferase from human placenta in complex with S-hexylglutathione at 2.8 A resolution. Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Huber, R. / Lo Bello, M. / Federici, G. / Parker, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pgt.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pgt.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/4pgt ftp://data.pdbj.org/pub/pdb/validation_reports/pg/4pgt | HTTPS FTP |
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-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: (0.933018, -0.145598, 0.329057), Vector: |
-Components
#1: Protein | Mass: 23379.742 Da / Num. of mol.: 2 / Mutation: VAL 104 VARIANT Source method: isolated from a genetically manipulated source Details: HGSTP1-1[V104] AND HGSTP1-1[I104] ARE NATURALLY OCCURRING VARIANTS OF HGSTP1-1 OBTAINED BY SITE-DIRECTED MUTAGENESIS Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 (DE3) PLYSS / Cellular location: CYTOPLASM / Gene: GTP_HUMAN / Organ: PLACENTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P09211, glutathione transferase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.13 Å3/Da / Density % sol: 42 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 4.3 MG/ML PROTEIN, 0.55 MM GSH CONJUGATE OF (+)-ANTI-BPDE, 0.8 M AMMONIUM SULFATE IN 50 MM MES BUFFER (PH 6.0). THE DROPS ...Details: CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 4.3 MG/ML PROTEIN, 0.55 MM GSH CONJUGATE OF (+)-ANTI-BPDE, 0.8 M AMMONIUM SULFATE IN 50 MM MES BUFFER (PH 6.0). THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING 1.6 M AMMONIUM SULFATE IN 0.1 M MES BUFFER (PH 6.0). | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 25842 / % possible obs: 90.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.87 |
Reflection shell | Resolution: 2.1→2.19 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 4.28 / % possible all: 81 |
Reflection | *PLUS Redundancy: 15 % |
Reflection shell | *PLUS % possible obs: 81 % |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / Num. parameters: 15337 / Num. restraintsaints: 14004 / Cross valid method: FREE R (AT EARLY STAGE) / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: X-PLOR WAS USED AT THE EARLY STAGE OF THE REFINEMENT.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3830.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.18 / Rfactor Rwork: 0.1896 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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