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- PDB-3gyk: The crystal structure of a thioredoxin-like oxidoreductase from S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gyk | ||||||
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Title | The crystal structure of a thioredoxin-like oxidoreductase from Silicibacter pomeroyi DSS-3 | ||||||
![]() | 27kDa outer membrane protein | ||||||
![]() | OXIDOREDUCTASE / APC61738.2 / Silicibacter pomeroyi DSS-3 / thioredoxin-like / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() Thioredoxin / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fan, Y. / Marshall, N. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of a thioredoxin-like oxidoreductase from Silicibacter pomeroyi DSS-3 Authors: Fan, Y. / Marshall, N. / Keigher, L. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.5 KB | Display | ![]() |
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PDB format | ![]() | 140.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.3 KB | Display | ![]() |
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Full document | ![]() | 479.4 KB | Display | |
Data in XML | ![]() | 36.8 KB | Display | |
Data in CIF | ![]() | 53.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN. IT IS PREDICTED TO BE MONOMERIC. |
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Components
#1: Protein | Mass: 19381.854 Da / Num. of mol.: 4 / Fragment: UNP residues 71-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Lithium sulfate, 0.1M Tris-HCl, 2.0M Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Mar 25, 2009 / Details: mirror |
Radiation | Monochromator: Si(111) crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97953 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. all: 71433 / Num. obs: 71433 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3518 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 14.254 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.8 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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