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Yorodumi- PDB-2wgr: Combining crystallography and molecular dynamics: The case of Sch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wgr | ||||||
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Title | Combining crystallography and molecular dynamics: The case of Schistosoma mansoni phospholipid glutathione peroxidase | ||||||
Components | GLUTATHIONE PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / SELENIUM / SELENOCYSTEINE / SCHISTOSOMIASIS / LIPID GSH PEROXIDASE / MOLECULAR DYNAMICS SIMULATIONS / ROS 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: 1.7 Å | ||||||
Authors | Dimastrogiovanni, D. / Anselmi, M. / Miele, A.E. / Boumis, G. / Angelucci, F. / Di Nola, A. / Brunori, M. / Bellelli, A. | ||||||
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 | 2wgr.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wgr.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wgr ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wgr | HTTPS FTP |
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-Related structure data
Related structure data | 2v1mSC 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: 19437.193 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q00277, glutathione peroxidase | ||
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#2: Chemical | ChemComp-POP / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | U43S MUTATION IN U43S SMGPX | |
-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: 48.5 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 0.2M NAH2PO4, 0.1M MES, 32% PEG-MME 5000, PH 6.0 |
-Data collection
Diffraction | Mean temperature: 199 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9185 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9185 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.31 Å / Num. obs: 21068 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V1M Resolution: 1.7→90.54 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 1.737 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.1 / 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: 10.591 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→90.54 Å
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Refine LS restraints |
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