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Open data
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Basic information
Entry | Database: PDB / ID: 7l8k | |||||||||||||||||||||||||||
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Title | Crystal structure of human GPX4-U46C | |||||||||||||||||||||||||||
![]() | Phospholipid hydroperoxide glutathione peroxidase | |||||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / alpha-beta protein | |||||||||||||||||||||||||||
Function / homology | ![]() 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 / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / Biosynthesis of aspirin-triggered D-series resolvins ...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 / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / arachidonic acid metabolic process / 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 / chromatin organization / nuclear envelope / cellular response to oxidative stress / spermatogenesis / response to oxidative stress / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Forouhar, F. / Liu, H. / Seibt, T. / Saneto, R. / Wigby, K. / Friedman, J. / Xia, X. / Shchepinov, M.S. / Ramesh, S. / Conrad, M. / Stockwell, B.R. | |||||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Patient-derived variant of GPX4 reveals the structural basis for its catalytic activity and degradation mechanism Authors: Liu, H. / Forouhar, F. / Seibt, T. / Saneto, R. / Wigby, K. / Friedman, J. / Xia, X. / Shchepinov, M.S. / Ramesh, S. / Conrad, M. / Stockwell, B.R. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l8lC ![]() 7l8mC ![]() 7l8qC ![]() 7l8rC ![]() 2obiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21888.098 Da / Num. of mol.: 1 / Mutation: U46C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 25.69 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.2 Details: 0.056 M sodium phosphate monobasic monohydrate and 1.344 M potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→34.46 Å / Num. obs: 29060 / % possible obs: 99.9 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 3 % / Num. unique obs: 1303 / CC1/2: 0.94 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OBI Resolution: 1.38→34.46 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 15.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.76 Å2 / Biso mean: 20.3969 Å2 / Biso min: 9.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.38→34.46 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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Refinement TLS params. | Method: refined / Origin x: 0.3268 Å / Origin y: -0.3355 Å / Origin z: 13.0064 Å
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Refinement TLS group |
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