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- PDB-4fyb: Structural and functional characterizations of a thioredoxin-fold... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fyb | ||||||
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Title | Structural and functional characterizations of a thioredoxin-fold protein from Helicobacter pylori | ||||||
![]() | Thiol:disulfide interchange protein (DsbC) | ||||||
![]() | OXIDOREDUCTASE / Thioredoxin fold / Reductase | ||||||
Function / homology | SoxW family / Thioredoxin-like domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Thiol:disulfide interchange protein (DsbC), putative![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoon, J.Y. / Kim, J. / Lee, S.J. / Im, H.N. / Kim, H.S. / Yoon, H. / An, D.R. / Kim, J.Y. / Kim, S. / Han, B.W. / Suh, S.W. | ||||||
![]() | ![]() Title: Structural and functional characterization of HP0377, a thioredoxin-fold protein from Helicobacter pylori Authors: Yoon, J.Y. / Kim, J. / An, D.R. / Lee, S.J. / Kim, H.S. / Im, H.N. / Yoon, H.J. / Kim, J.Y. / Kim, S.J. / Han, B.W. / Suh, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.1 KB | Display | ![]() |
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PDB format | ![]() | 62 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 457 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27548.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.04 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 200mM potassium acetate (pH 7.8), 20% (w/v) polyethylene glycol (PEG) 1500, 2.2mM FOS-Choline-8 (fluorinated), VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 22650 / Num. obs: 22514 / % possible obs: 99.4 % |
Reflection shell | Resolution: 2.2→2.28 Å |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 42.383 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.198→2.255 Å / Total num. of bins used: 20
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