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Yorodumi- PDB-3d4t: Crystal structure of the periplasmic thioredoxin SoxS from Paraco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d4t | ||||||
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Title | Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (oxidized form) | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin / sulfur oxidation | ||||||
Function / homology | Thioredoxin-like domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / BETA-MERCAPTOETHANOL / Thioredoxin-like fold domain-containing protein Function and homology information | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Carius, Y. / Friedrich, C.G. / Scheidig, A.J. | ||||||
Citation | Journal: To be Published 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. / Orawski, G. / Bardischewsky, F. / Quentmeier, A. / Rother, D. / Friedrich, C.G. / Scheidig, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d4t.cif.gz | 35.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d4t.ent.gz | 23.5 KB | Display | PDB format |
PDBx/mmJSON format | 3d4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/3d4t ftp://data.pdbj.org/pub/pdb/validation_reports/d4/3d4t | HTTPS FTP |
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-Related structure data
-Links
-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: 13080.744 Da / Num. of mol.: 1 / Fragment: periplasmic domain, UNP residues 32-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: GB17 / Gene: soxS / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q8KM22 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 0.1M citrate, 0.4M sodium phosphate, 0.4M potassium phosphate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: OXFORD DIFFRACTION ENHANCED ULTRA / Wavelength: 1.5418 |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Mar 7, 2006 / Details: mirrors |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→12.04 Å / Num. all: 8063 / Num. obs: 7981 / % possible obs: 99.52 % / Redundancy: 33.61 % / Biso Wilson estimate: 17.26 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 36.02 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 19.65 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 6.15 / Num. unique all: 1152 / Rsym value: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: derived from SoxS MAD data Resolution: 2.05→12.04 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.948 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.155 / 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: 16.424 Å2
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Refine analyze | Luzzati coordinate error free: 0.155 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→12.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.102 Å / Total num. of bins used: 20
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