+Open data
-Basic information
Entry | Database: PDB / ID: 4gss | ||||||
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Title | HUMAN GLUTATHIONE S-TRANSFERASE P1-1 Y108F MUTANT | ||||||
Components | GLUTATHIONE S-TRANSFERASE | ||||||
Keywords | TRANSFERASE / MULTIGENE FAMILY | ||||||
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 / glutathione derivative biosynthetic process / hepoxilin 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 / glutathione derivative biosynthetic process / hepoxilin 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 / JUN kinase binding / Paracetamol ADME / 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 fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / xenobiotic metabolic process / glutathione metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / fatty acid binding / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to lipopolysaccharide / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Oakley, A. / Rossjohn, J. / Parker, M. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Multifunctional role of Tyr 108 in the catalytic mechanism of human glutathione transferase P1-1. Crystallographic and kinetic studies on the Y108F mutant enzyme. Authors: Lo Bello, M. / Oakley, A.J. / Battistoni, A. / Mazzetti, A.P. / Nuccetelli, M. / Mazzarese, G. / Rossjohn, J. / Parker, M.W. / Ricci, G. #1: 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 | 4gss.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gss.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gss_validation.pdf.gz | 806.6 KB | Display | wwPDB validaton report |
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Full document | 4gss_full_validation.pdf.gz | 813.4 KB | Display | |
Data in XML | 4gss_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 4gss_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/4gss ftp://data.pdbj.org/pub/pdb/validation_reports/gs/4gss | HTTPS FTP |
-Related structure data
Related structure data | 1gssS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.939803, 0.130846, 0.315673), Vector: |
-Components
#1: Protein | Mass: 23230.570 Da / Num. of mol.: 2 / Mutation: Y108F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTP_HUMAN / Organ: PLACENTA / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.83 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / 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: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 6, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. obs: 14346 / % possible obs: 88.5 % / Redundancy: 5.57 % / Biso Wilson estimate: 39.2 Å2 / Rsym value: 0.111 / Net I/σ(I): 7.73 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.291 / % possible all: 90 |
Reflection | *PLUS Num. measured all: 79944 / Rmerge(I) obs: 0.111 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.291 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GSS Resolution: 2.5→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 28.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Weight Biso : 1 / Weight position: 1000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 |