[English] 日本語
Yorodumi- PDB-1gp1: THE REFINED STRUCTURE OF THE SELENOENZYME GLUTATHIONE PEROXIDASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gp1 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | THE REFINED STRUCTURE OF THE SELENOENZYME GLUTATHIONE PEROXIDASE AT 0.2-NM RESOLUTION | ||||||||||||
Components | GLUTATHIONE PEROXIDASE | ||||||||||||
Keywords | OXIDOREDUCTASE(H2O2(A)) | ||||||||||||
Function / homology | Function and homology information positive regulation of supramolecular fiber organization / endothelial cell development / phospholipid-hydroperoxide glutathione peroxidase activity / response to symbiotic bacterium / glutathione peroxidase / regulation of mammary gland epithelial cell proliferation / lipoxygenase pathway / protein oxidation / Lewy body / arachidonic acid metabolic process ...positive regulation of supramolecular fiber organization / endothelial cell development / phospholipid-hydroperoxide glutathione peroxidase activity / response to symbiotic bacterium / glutathione peroxidase / regulation of mammary gland epithelial cell proliferation / lipoxygenase pathway / protein oxidation / Lewy body / arachidonic acid metabolic process / blood vessel endothelial cell migration / skeletal muscle tissue regeneration / response to selenium ion / UV protection / angiogenesis involved in wound healing / glutathione peroxidase activity / triglyceride metabolic process / response to hydroperoxide / biological process involved in interaction with symbiont / myoblast proliferation / temperature homeostasis / heart contraction / fat cell differentiation / negative regulation of release of cytochrome c from mitochondria / regulation of proteasomal protein catabolic process / glutathione metabolic process / skeletal muscle fiber development / epigenetic regulation of gene expression / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of inflammatory response to antigenic stimulus / cell redox homeostasis / hydrogen peroxide catabolic process / response to gamma radiation / sensory perception of sound / peroxidase activity / response to hydrogen peroxide / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / SH3 domain binding / vasodilation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to xenobiotic stimulus / mitochondrion / cytosol Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||||||||
Authors | Epp, O. / Ladenstein, R. | ||||||||||||
Citation | Journal: Eur.J.Biochem. / Year: 1983 Title: The refined structure of the selenoenzyme glutathione peroxidase at 0.2-nm resolution. Authors: Epp, O. / Ladenstein, R. / Wendel, A. #1: Journal: J.Mol.Biol. / Year: 1979 Title: Structure Analysis and Molecular Model of the Selenoenzyme Glutathione Peroxidase at 2.8 Angstroms Resolution Authors: Ladenstein, R. / Epp, O. / Bartels, K. / Jones, A. / Huber, R. / Wendel, A. #2: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1984 Title: The Amino-Acid Sequence of Bovine Glutathione Peroxidase Authors: Guenzler, W.A. / Steffens, G.J. / Grossmann, A. / Kim, S.-M.A. / Oetting, F. / Wendel, A. / Flohe, L. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gp1.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gp1.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gp1 ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gp1 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: SEE REMARK 7. / 2: RESIDUES 97 AND 150 OF EACH CHAIN ARE CIS PROLINES. / 3: SEE REMARK 6. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.131858, -0.010348, 0.991227), Vector: |
-Components
#1: Protein | Mass: 21965.893 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: ERYTHROCYTERed blood cell / References: UniProt: P00435, glutathione peroxidase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.99 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7.2 / Method: microdialysis | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 26564 / % possible obs: 71 % / Num. measured all: 93223 / Rmerge(I) obs: 0.101 |
-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→6 Å / Rfactor Rwork: 0.171 Details: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 24798 / Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |