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- PDB-5jy5: Crystal structure of Thioredoxin 1 from Cryptococcus neoformans a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jy5 | |||||||||
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Title | Crystal structure of Thioredoxin 1 from Cryptococcus neoformans at 1.8 Angstroms resolution | |||||||||
![]() | Thioredoxin | |||||||||
![]() | OXIDOREDUCTASE / Thioredoxin 1 Cryptococcus neoformans X-ray crystallography | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bravo-Chaucanes, C.P. / Abadio, A.K.R. / Kioshima, E.S. / Felipe, M.S.S. / Barbosa, J.A.R.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Thioredoxin 1 from Cryptococcus neoformans at 1.8 Angstroms resolution Authors: Bravo-Chaucanes, C.P. / Abadio, A.K.R. / Kioshima, E.S. / Felipe, M.S.S. / Barbosa, J.A.R.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.3 KB | Display | ![]() |
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PDB format | ![]() | 81.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473 KB | Display | ![]() |
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Full document | ![]() | 476.7 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j23S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12294.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02801 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.13 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 1.6 M ammonium sulfate, 0.02 M tris hydrochloride / PH range: 7.6-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 31224 / % possible obs: 100 % / Redundancy: 37.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 52.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 34.7 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 6.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2J23 Resolution: 1.8→95.87 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.413 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.095 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.274 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→95.87 Å
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Refine LS restraints |
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