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Yorodumi- PDB-3tco: Crystallographic and spectroscopic characterization of Sulfolobus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tco | ||||||
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Title | Crystallographic and spectroscopic characterization of Sulfolobus solfataricus TrxA1 provide insights into the determinants of thioredoxin fold stability | ||||||
Components | Thioredoxin (TrxA-1) | ||||||
Keywords | OXIDOREDUCTASE / disulfide oxidoreductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Esposito, L. / Ruggiero, A. / Masullo, M. / Ruocco, M.R. / Lamberti, A. / Arcari, P. / Zagari, A. / Vitagliano, L. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Crystallographic and spectroscopic characterizations of Sulfolobus solfataricus TrxA1 provide insights into the determinants of thioredoxin fold stability. Authors: Esposito, L. / Ruggiero, A. / Masullo, M. / Ruocco, M.R. / Lamberti, A. / Arcari, P. / Zagari, A. / Vitagliano, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tco.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tco.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 3tco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/3tco ftp://data.pdbj.org/pub/pdb/validation_reports/tc/3tco | HTTPS FTP |
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-Related structure data
Related structure data | 3hhvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 12466.255 Da / Num. of mol.: 3 / Fragment: Truncated form (25-133) of Thioredoxin (TrxA-1) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: trxA-1, SSO0368 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980E5 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% (w/v) PEG4000; 0.2 M Ammonium sulfate. Protein concentration 2-6 mg/ml., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 12, 2009 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→23 Å / Num. all: 28596 / Num. obs: 26928 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.2 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HHV Resolution: 1.9→22.48 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 273255.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.3096 Å2 / ksol: 0.409449 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→22.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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