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- PDB-6bwt: 2.45 Angstrom Resolution Crystal Structure Thioredoxin Reductase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bwt | ||||||
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Title | 2.45 Angstrom Resolution Crystal Structure Thioredoxin Reductase from Francisella tularensis. | ||||||
![]() | Thioredoxin reductase | ||||||
![]() | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Thioredoxin Reductase | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 2.45 Angstrom Resolution Crystal Structure Thioredoxin Reductase from Francisella tularensis. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 436.4 KB | Display | ![]() |
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PDB format | ![]() | 359.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.9 KB | Display | ![]() |
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Full document | ![]() | 473.6 KB | Display | |
Data in XML | ![]() | 40.8 KB | Display | |
Data in CIF | ![]() | 57.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tdeS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 34303.902 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SCHU S4 / Schu 4 / Gene: trxB, FTT_0489c / Plasmid: pMCSG7 / Production host: ![]() ![]() References: UniProt: Q5NHG5, thioredoxin-disulfide reductase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 7.7 mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCL pH 8.3; Screen: Clssics II (F8), 0.2M Ammonium sulfate, 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2010 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 41167 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.029 / Rrim(I) all: 0.067 / Rsym value: 0.06 / Χ2: 1.014 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2009 / CC1/2: 0.717 / Rpim(I) all: 0.363 / Rrim(I) all: 0.818 / Rsym value: 0.73 / Χ2: 0.994 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TDE Resolution: 2.45→29.52 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 18.487 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.751 / ESU R Free: 0.296 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.212 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→29.52 Å
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Refine LS restraints |
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