+Open data
-Basic information
Entry | Database: PDB / ID: 2i3y | ||||||
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Title | Crystal structure of human glutathione peroxidase 5 | ||||||
Components | Epididymal secretory glutathione peroxidase | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin fold / Epididymal androgen related protein / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information glutathione peroxidase / glutathione peroxidase activity / Detoxification of Reactive Oxygen Species / peroxidase activity / lipid metabolic process / cellular response to oxidative stress / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kavanagh, K.L. / Johansson, C. / Rojkova, A. / Umeano, C. / Bunkoczi, G. / Gileadi, O. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. ...Kavanagh, K.L. / Johansson, C. / Rojkova, A. / Umeano, C. / Bunkoczi, G. / Gileadi, O. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be published Title: Crystal structure of human glutathione peroxidase 5 Authors: Kavanagh, K.L. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i3y.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i3y.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 2i3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/2i3y ftp://data.pdbj.org/pub/pdb/validation_reports/i3/2i3y | 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 by: 1 1 1 x,-y, -z -x+1, -y, z -x+1, y,-z |
-Components
#1: Protein | Mass: 24586.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPX5 / Plasmid: pNIC-bsa4 (pET derivative) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75715, glutathione peroxidase |
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#2: Chemical | ChemComp-EDO / |
#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: 2.3 Å3/Da / Density % sol: 46.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 3350, 0.2 M sodium formate, 5% ETHYLENE GLYCOL, pH 8, 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: 0.8983 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 19, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8983 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 16114 / Num. obs: 16114 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2305 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2F8A Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.868 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.15 / 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: 37.321 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 71.6569 Å / Origin y: 18.2926 Å / Origin z: 3.0418 Å
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