+Open data
-Basic information
Entry | Database: PDB / ID: 2v1m | |||||||||
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Title | Crystal structure of Schistosoma mansoni glutathione peroxidase | |||||||||
Components | GLUTATHIONE PEROXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / SELENIUM / SELENOCYSTEINE / LIPID PEROXIDASE / SCHISTOSOMA DETOXIFICATION PATHWAY | |||||||||
Function / homology | Function and homology information phospholipid-hydroperoxide glutathione peroxidase activity / glutathione peroxidase / glutathione peroxidase activity / cellular response to oxidative stress / mitochondrion / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | SCHISTOSOMA MANSONI (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | |||||||||
Authors | Dimastrogiovanni, D. / Miele, A.E. / Angelucci, F. / Boumis, G. / Bellelli, A. / Brunori, M. | |||||||||
Citation | Journal: Proteins / Year: 2010 Title: Combining Crystallography and Molecular Dynamics: The Case of Schistosoma Mansoni Phospholipid Glutathione Peroxidase. Authors: Dimastrogiovanni, D. / Anselmi, M. / Miele, A.E. / Boumis, G. / Petersson, L. / Angelucci, F. / Nola, A.D. / Brunori, M. / Bellelli, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v1m.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v1m.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1m ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1m | HTTPS FTP |
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-Related structure data
Related structure data | 2wgrC 2obiS S: Starting model for refinement C: citing same article (ref.) |
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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: 19501.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Description: ADULT MIXED SEX CDNA / Plasmid: PGEX4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q00277, glutathione peroxidase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-LI / | #5: Water | ChemComp-HOH / | Nonpolymer details | CYSTEINE SULPHONIC ACID (OCS): OXIDIZED CYSTEINE RESIDUE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 31.7 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2M LISULFATE, 0.2M NAACETATE, PH 4.5, 24% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 1→41.38 Å / Num. obs: 81445 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 4.97 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1→1.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OBI Resolution: 1→62.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.939 / SU B: 0.479 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL RESIDUES 1-6 ARE DISORDERED AND NOT INCLUDED IN THE MODEL
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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: 6.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1→62.5 Å
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Refine LS restraints |
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