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Yorodumi- PDB-2gs3: Crystal structure of the selenocysteine to glycine mutant of huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gs3 | ||||||
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Title | Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 4(GPX4) | ||||||
Components | Phospholipid hydroperoxide glutathione peroxidase | ||||||
Keywords | OXIDOREDUCTASE / GPX4 / GSHPX-4 / phospholipid hydroperoxide / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Johansson, C. / Kavanagh, K.L. / Rojkova, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 4(GPX4) Authors: Johansson, C. / Kavanagh, K.L. / Rojkova, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gs3.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gs3.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gs3 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gs3 | HTTPS FTP |
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-Related structure data
Related structure data | 2f8aS 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: 21184.301 Da / Num. of mol.: 1 / Mutation: SeCys73Gly Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase |
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#2: Chemical | ChemComp-CL / |
#3: 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: 4.58 Å3/Da / Density % sol: 73.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 20% PEG 3350, 0.2 M ammonium chloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 32109 / Num. obs: 32109 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4550 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F8A Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.242 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.082 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.285 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.3155 Å / Origin y: 26.1899 Å / Origin z: 15.5517 Å
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