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Yorodumi- PDB-2obi: Crystal structure of the Selenocysteine to Cysteine Mutant of hum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2obi | ||||||
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Title | Crystal structure of the Selenocysteine to Cysteine Mutant of human phospholipid hydroperoxide glutathione peroxidase (GPx4) | ||||||
Components | Phospholipid hydroperoxide glutathione peroxidase (GPX4) | ||||||
Keywords | OXIDOREDUCTASE / HUMAN GPX4 / PEROXIDASE / SELENOPROTEIN / THIOREDOXIN-FOLD / ANTI-OXIDATVE DEFENSE SYSTEM | ||||||
Function / homology | Function and homology information phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / negative regulation of ferroptosis / selenium binding / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / arachidonic acid metabolic process ...phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / negative regulation of ferroptosis / selenium binding / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / arachidonic acid metabolic process / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / glutathione peroxidase activity / long-chain fatty acid biosynthetic process / protein polymerization / phospholipid metabolic process / response to estradiol / nuclear envelope / chromatin organization / spermatogenesis / response to oxidative stress / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Scheerer, P. / Krauss, N. / Hoehne, W. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structural basis for catalytic activity and enzyme polymerization of phospholipid hydroperoxide glutathione peroxidase-4 (GPx4). Authors: Scheerer, P. / Borchert, A. / Krauss, N. / Wessner, H. / Gerth, C. / Hohne, W. / Kuhn, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2obi.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2obi.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 2obi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/2obi ftp://data.pdbj.org/pub/pdb/validation_reports/ob/2obi | HTTPS FTP |
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-Related structure data
Related structure data | 1gp1S 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
#1: Protein | Mass: 20955.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 8000, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 29, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 35135 / Num. obs: 35135 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 18.68 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 32.07 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.0364 / Mean I/σ(I) obs: 2.48 / Num. unique all: 2429 / Rsym value: 0.0364 / % possible all: 66.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GP1 Resolution: 1.55→30.69 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 8.514 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→30.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å
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