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Yorodumi- PDB-2xc2: Crystal structure of oxidized Schistosoma mansoni Thioredoxin pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xc2 | ||||||
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Title | Crystal structure of oxidized Schistosoma mansoni Thioredoxin pre- protein at 1.6 Angstrom | ||||||
Components | THIOREDOXINN | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN DISULFIDE REDUCTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SCHISTOSOMA MANSONI (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Boumis, G. / Miele, A.E. / Dimastrogiovanni, D. / Angelucci, F. / Bellelli, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Structural and Functional Characterization of Schistosoma Mansoni Thioredoxin. Authors: Boumis, G. / Angelucci, F. / Bellelli, A. / Brunori, M. / Dimastrogiovanni, D. / Miele, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xc2.cif.gz | 39.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xc2.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xc2_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 2xc2_full_validation.pdf.gz | 423.9 KB | Display | |
Data in XML | 2xc2_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 2xc2_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xc2 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xc2 | HTTPS FTP |
-Related structure data
Related structure data | 2xbiC 2xbqC 1xwaS C: citing same article (ref.) 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: 13100.223 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Description: CDNA FROM ADULT SCHISTOSOMA MANSONI / Plasmid: PGEX-4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8T9N5, protein-disulfide reductase | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | GSPEFTS AT N-TERMINUS CAME FROM THROMBIN CLEAVAGE OF THE EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 41.86 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M SODIUM CACODYLATE PH 6.5, 10MM ZINC ACETATE, 24% (W/V) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.932 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→39.1 Å / Num. obs: 15044 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.56→1.61 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.1 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XWA Resolution: 1.56→39.1 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.83 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / 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: 18.614 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→39.1 Å
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Refine LS restraints |
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