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Yorodumi- PDB-4ruv: Crystal structure of thioredoxin 2 from Staphylococcus aureus NCTC8325 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ruv | ||||||
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Title | Crystal structure of thioredoxin 2 from Staphylococcus aureus NCTC8325 | ||||||
Components | Thioredoxin | ||||||
Keywords | OXIDOREDUCTASE / electron transport | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / protein-disulfide reductase (NAD(P)H) activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å | ||||||
Authors | Bose, M. / Biswas, R. / Roychowdhury, A. / Bhattacharyya, S. / Ghosh, A.K. / Das, A.K. | ||||||
Citation | Journal: Biochimie / Year: 2019 Title: Elucidation of the mechanism of disulfide exchange between staphylococcal thioredoxin2 and thioredoxin reductase2: A structural insight. Authors: Bose, M. / Bhattacharyya, S. / Biswas, R. / Roychowdhury, A. / Bhattacharjee, A. / Ghosh, A.K. / Das, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ruv.cif.gz | 36 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ruv.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ruv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/4ruv ftp://data.pdbj.org/pub/pdb/validation_reports/ru/4ruv | HTTPS FTP |
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-Related structure data
Related structure data | 6a4jC 2fa4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13124.634 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC8325 / Gene: SAOUHSC_00834 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q2G000 |
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#2: 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: 1.78 Å3/Da / Density % sol: 30.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Na-HEPES pH 7.5, 1.4 M sodium citrate tribasic dihydrate , VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 15, 2014 / Details: varimax | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.926→18.92 Å / Num. all: 6850 / Num. obs: 6850 / % possible obs: 98.2 % / Redundancy: 3.5 % / Rsym value: 0.115 / Net I/σ(I): 6.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FA4 Resolution: 1.93→18.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.138 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1806 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.175 / 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: 18.157 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→18.92 Å
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Refine LS restraints |
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