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Yorodumi- PDB-3vi7: Human hematopoietic prostaglandin D synthase inhibitor complex st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vi7 | ||||||
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Title | Human hematopoietic prostaglandin D synthase inhibitor complex structures | ||||||
Components | Hematopoietic prostaglandin D synthase | ||||||
Keywords | Isomerase/Isomerase Inhibitor / sigma class glutathione S transferase(GST) / isomerase / glutathione S transferase / Ca binding / GSH binding / Prostaglandin H2 binding / Isomerase-Isomerase Inhibitor complex | ||||||
Function / homology | Function and homology information prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior ...prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior / intracellular membrane-bounded organelle / calcium ion binding / magnesium ion binding / signal transduction / protein homodimerization activity / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kado, Y. / Inoue, T. | ||||||
Citation | Journal: J.Biochem. / Year: 2012 Title: Human hematopoietic prostaglandin D synthase inhibitor complex structures Authors: Kado, Y. / Aritake, K. / Uodome, N. / Okano, Y. / Okazaki, N. / Matsumura, H. / Urade, Y. / Inoue, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vi7.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vi7.ent.gz | 155.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/3vi7 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/3vi7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23256.730 Da / Num. of mol.: 4 / Mutation: N144M/N344M/N544M/N744M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPGDS, GSTS, PGDS, PTGDS2 / Production host: Escherichia coli (E. coli) References: UniProt: O60760, prostaglandin-D synthase, glutathione transferase #2: Chemical | ChemComp-GSH / #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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: PEG6000, Tris-HCl, CaCl2, GSH, DTT, 1,4-dioxane,, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2003 |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 57344 / Num. obs: 56268 / % possible obs: 98.1 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.106 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.7 Å2 / Biso mean: 23.0094 Å2 / Biso min: 3.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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