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- PDB-3dml: Crystal structure of the periplasmic thioredoxin SoxS from Paraco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dml | ||||||
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Title | Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (reduced form) | ||||||
![]() | Putative uncharacterized protein | ||||||
![]() | OXIDOREDUCTASE / thioredoxin / sulfur oxidation / thiol-disulfide oxidoreductase | ||||||
Function / homology | Thioredoxin-like domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Thioredoxin-like fold domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carius, Y. / Friedrich, C.G. / Scheidig, A.J. | ||||||
![]() | ![]() Title: Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus indicates a dual Trx/Grx functionality for activation of chemotrophic sulfur oxidation in vivo Authors: Carius, Y. / Rother, D. / Friedrich, C.G. / Scheidig, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.4 KB | Display | ![]() |
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PDB format | ![]() | 25.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.5 KB | Display | ![]() |
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Full document | ![]() | 431.9 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 11.2 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13315.221 Da / Num. of mol.: 1 / Fragment: periplasmic domain, UNP residues 32-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8KM22, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1M citrate, 0.4M sodium phosphate, 0.4M potassium phosphate, 3% (w/v) glucose, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2006 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Double crystal Si[111] / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→20.71 Å / Num. all: 10064 / Num. obs: 9998 / % possible obs: 99.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 18.37 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 30.87 | |||||||||||||||
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 6.36 / Num. unique all: 662 / Rsym value: 0.447 / % possible all: 97.9 |
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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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.168 Å2
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Refine analyze | Luzzati coordinate error free: 0.124 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 Å / Total num. of bins used: 20
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