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Yorodumi- PDB-2he3: Crystal structure of the selenocysteine to cysteine mutant of hum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2he3 | ||||||
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Title | Crystal structure of the selenocysteine to cysteine mutant of human glutathionine peroxidase 2 (GPX2) | ||||||
Components | Glutathione peroxidase 2 | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin fold / gastrointestinal glutathione peroxidase 2 / GPRP / GSHPX-GI / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase activity / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to oxidative stress / electron transfer activity ...Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase activity / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to oxidative stress / electron transfer activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 cysteine mutant of human glutathionine peroxidase 2 (GPX2) Authors: Kavanagh, K.L. / Oppermann, U. | ||||||
History |
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Remark 999 | SEQUENCE THERES IS A SELENOCYSTEINE TO CYSTEINE MUTATION AT RESIDUE 40. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2he3.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2he3.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 2he3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/2he3 ftp://data.pdbj.org/pub/pdb/validation_reports/he/2he3 | 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 on special symmetry positions |
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Details | The biological assembly is a tetramer generated from the monomer in the AU by the operations: -x,-y,z; x,-y,-z+1; -x,y,-z+1 |
-Components
#1: Protein | Mass: 24115.377 Da / Num. of mol.: 1 / Mutation: S15N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPX2 / Plasmid: pNIC-Bsa4 (pET derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P18283, glutathione peroxidase | ||
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#2: Chemical | #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: 3.01 Å3/Da / Density % sol: 59.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 200 mM sodium formate, 100 mM Bis-Tris propane, 10% ethylene glycol, pH 7.5, 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: 0.9183 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 18, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9183 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42 Å / Num. all: 17619 / Num. obs: 17619 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2496 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2f8a Resolution: 2.1→42 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.015 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.138 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.278 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.273 Å / Origin y: 18.3957 Å / Origin z: 41.5865 Å
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