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Yorodumi- PDB-7jyp: Structure of thioredoxin reductase from the thermophilic eubacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jyp | ||||||
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Title | Structure of thioredoxin reductase from the thermophilic eubacterium Thermosipho africanus TCF52B | ||||||
Components | Thioredoxin reductase | ||||||
Keywords | OXIDOREDUCTASE / Thioredoxin reductase / thermophile / Thermosipho africanus / protein stability / catalysis / NADH | ||||||
Function / homology | Function and homology information thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cytoplasm Similarity search - Function | ||||||
Biological species | Thermosipho africanus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sahtout, N. / Kuttiyatveetil, J.R.A. / Sanders, D.A.R. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To be Published Title: Structure of thioredoxin reductase from the thermophilic eubacterium Thermosipho africanus TCF52B. Authors: Sahtout, N. / Kuttiyatveetil, J.R.A. / Sanders, D.A.R. #1: Journal: Biochim Biophys Acta Proteins Proteom / Year: 2019 Title: Structure and function of the putative thioredoxin 1 from the thermophilic eubacterium Thermosipho africanus strain TCF52B. Authors: Sahtout, N. / Kuttiyatveetil, J.R.A. / Sanders, D.A.R. #2: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016 Title: Putative thioredoxin Trx1 from Thermosipho africanus strain TCF52B: expression, purification and structural determination using S-SAD. Authors: Sahtout, N. / Kuttiyatveetil, J.R. / Fodje, M. / Sanders, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jyp.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jyp.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 7jyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jyp_validation.pdf.gz | 1004.1 KB | Display | wwPDB validaton report |
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Full document | 7jyp_full_validation.pdf.gz | 1006 KB | Display | |
Data in XML | 7jyp_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 7jyp_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/7jyp ftp://data.pdbj.org/pub/pdb/validation_reports/jy/7jyp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37443.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosipho africanus (strain TCF52B) (bacteria) Strain: TCF52B / Gene: trxB, THA_1385 / Plasmid: pEHISTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: B7ICV3, thioredoxin-disulfide reductase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.15 % / Description: yellow rhomboid shaped crystals |
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Crystal grow | Temperature: 289 K / Method: microbatch Details: 0.2 M Ammonium Chloride, 20 % (w/v) PEG 3350, 0.1 M b-Nicotinamide adenine dinucleotide (NAD) hydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.12 Å / Num. obs: 42842 / % possible obs: 99.2 % / Redundancy: 9.2 % / Biso Wilson estimate: 25.76 Å2 / CC1/2: 0.999 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.6→1.657 Å / Num. unique obs: 3980 / CC1/2: 0.17 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Automated Resolution: 1.6→48.119 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→48.119 Å
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Refine LS restraints |
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LS refinement shell |
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