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Yorodumi- PDB-6mos: Structure of thioredoxin 1 from the thermophilic eubacterium Ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mos | ||||||
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Title | Structure of thioredoxin 1 from the thermophilic eubacterium Thermosipho africanus TCF52B | ||||||
Components | Thioredoxin | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin / thermophile / Thermosipho africanus / protein stability / catalysis | ||||||
Function / homology | Thioredoxin / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin Function and homology information | ||||||
Biological species | Thermosipho africanus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80013732031 Å | ||||||
Authors | Sahtout, N. / Kuttiyatveetil, J.R. / Sanders, D.A.R. | ||||||
Citation | 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. #1: 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 | 6mos.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mos.ent.gz | 20.7 KB | Display | PDB format |
PDBx/mmJSON format | 6mos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mos_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 6mos_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 6mos_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 6mos_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/6mos ftp://data.pdbj.org/pub/pdb/validation_reports/mo/6mos | 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: 13848.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosipho africanus (strain TCF52B) (bacteria) Strain: TCF52B / Gene: THA_37 / Cell line (production host): BL21-CodonPlus-RIL / Production host: Escherichia coli (E. coli) / References: UniProt: B7IEN1 |
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#2: Chemical | ChemComp-TAM / |
#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: 1.67 Å3/Da / Density % sol: 26.55 % / Description: large irregular-shaped trapezoid crystals |
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Crystal grow | Temperature: 289 K / Method: microbatch Details: 0.2 M MgCl2 , 0.1 M bis-tris pH 6.5, 25%(w/v) PEG 3350 |
-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: Dec 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.02 Å / Num. obs: 8989 / % possible obs: 99.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.4388546055 Å2 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 7.3 / Num. unique obs: 1198 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.80013732031→33.0566043115 Å / SU ML: 0.154539013252 / Cross valid method: NONE / σ(F): 1.33595773055 / Phase error: 30.8445965544
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5232942362 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.80013732031→33.0566043115 Å
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Refine LS restraints |
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LS refinement shell |
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