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Yorodumi- PDB-2xbi: Crystal structure of Schistosoma mansoni Thioredoxin at 1.6 Angstrom -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xbi | ||||||
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Title | Crystal structure of Schistosoma mansoni Thioredoxin at 1.6 Angstrom | ||||||
Components | THIOREDOXIN | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN DISULFIDE REDUCTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SCHISTOSOMA MANSONI (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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. #1: Journal: J.Biol.Chem. / Year: 2010 Title: Mapping the Catalytic Cycle of Schistosoma Mansoni Thioredoxin Glutathione Reductase by X-Ray Crystallography. Authors: Angelucci, F. / Dimastrogiovanni, D. / Boumis, G. / Brunori, M. / Miele, A.E. / Saccoccia, F. / Bellelli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xbi.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xbi.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xbi_validation.pdf.gz | 422.6 KB | Display | wwPDB validaton report |
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Full document | 2xbi_full_validation.pdf.gz | 422.6 KB | Display | |
Data in XML | 2xbi_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 2xbi_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/2xbi ftp://data.pdbj.org/pub/pdb/validation_reports/xb/2xbi | HTTPS FTP |
-Related structure data
Related structure data | 2xbqC 2xc2C 1xwaS 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: 12085.128 Da / Num. of mol.: 1 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-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | GS AT N-TERMINUS COME 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: 2.13 Å3/Da / Density % sol: 42.2 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M BISTRIS, PH 6.5, 45% POLYPROPYLENE GLYCOL P400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→36.01 Å / Num. obs: 14224 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.7 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XWA Resolution: 1.6→36.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 1.809 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / 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: 9.734 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→36.01 Å
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Refine LS restraints |
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