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Yorodumi- PDB-3hjo: Crystal Structure of Glutathione Transferase Pi Y108V Mutant in C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hjo | ||||||
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Title | Crystal Structure of Glutathione Transferase Pi Y108V Mutant in Complex with the Glutathione Conjugate of Ethacrynic Acid | ||||||
Components | Glutathione S-transferase P | ||||||
Keywords | TRANSFERASE / glutathione / detoxification / ethacrynic acid / ethacrynic acid-glutathione conjugate | ||||||
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: 1.95 Å | ||||||
Authors | Parker, L.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Influence of the H-site residue 108 on human glutathione transferase P1-1 ligand binding: structure-thermodynamic relationships and thermal stability. Authors: Quesada-Soriano, I. / Parker, L.J. / Primavera, A. / Casas-Solvas, J.M. / Vargas-Berenguel, A. / Baron, C. / Morton, C.J. / Mazzetti, A.P. / Lo Bello, M. / Parker, M.W. / Garcia-Fuentes, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hjo.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hjo.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 3hjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hjo_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3hjo_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3hjo_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3hjo_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/3hjo ftp://data.pdbj.org/pub/pdb/validation_reports/hj/3hjo | HTTPS FTP |
-Related structure data
Related structure data | 3hjmC 3hkrC 5gssS C: citing same article (ref.) 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23182.527 Da / Num. of mol.: 2 / Mutation: Y108V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1 / Plasmid: pSE420 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P09211, glutathione transferase |
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-Non-polymers , 5 types, 485 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | #6: 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: 2.51 Å3/Da / Density % sol: 51.06 % / Mosaicity: 0.527 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 133mM Calcium Acetate, 18% PEG8000, 100mM MES, pH5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 13, 2008 / Details: AXCO |
Radiation | Monochromator: AXCO Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→37.54 Å / Num. obs: 29135 / % possible obs: 87.2 % / Redundancy: 5.6 % / Biso Wilson estimate: 16.32 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 8.56 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / Num. measured all: 7177 / Num. unique all: 2026 / Rsym value: 0.38 / % possible all: 42.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5GSS Resolution: 1.95→37.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.143 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.885 / SU B: 3.106 / SU ML: 0.091 / SU R Cruickshank DPI: 0.177 / SU Rfree: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.24 Å2 / Biso mean: 14.39 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→37.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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