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Open data
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Basic information
Entry | Database: PDB / ID: 1o8x | ||||||
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Title | Mutant tryparedoxin-I Cys43Ala | ||||||
![]() | TRYPAREDOXIN | ||||||
![]() | ELECTRON TRANSPORT / TRYPAREDOXIN-I / SYNCHROTRON RADIATION / DISULFIDE BONDS TRYPAREDOXIN / CRITHIDIA FASCICULATA / THIOREDOXIN / TRYPANOSOME / ANOMALOUS DISPERSION / OXIDATIVE STRESS / OXIDOREDUCTASE | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / negative regulation of protein ubiquitination / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alphey, M.S. / Bond, C.S. / Hunter, W.N. | ||||||
![]() | ![]() Title: Tryparedoxins from Crithidia Fasciculata and Trypanosoma Brucei: Photoreduction of the Redox Disulfide Using Synchrotron Radiation and Evidence for a Conformational Switch Implicated in Function Authors: Alphey, M.S. / Gabrielsen, M. / Micossi, E. / Leonard, G. / Mcsweeney, S.M. / Ravelli, R.B.G. / Tetaud, E. / Fairlamb, A.H. / Bond, C.S. / Hunter, W.N. #1: ![]() Title: The High Resolution Structure of Recombinant Crithidia Fasciculata Tryparedoxin-I Authors: Alphey, M.S. / Leonard, G. / Gourley, D.G. / Tetaud, E. / Fairlamb, A.H. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.4 KB | Display | ![]() |
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Full document | ![]() | 409.4 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o73C ![]() 1o7uC ![]() 1o85C ![]() 1o8wC ![]() 1oc8C ![]() 1oc9C ![]() 1qk8S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 16466.568 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 42.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.2 / Details: pH 8.20 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Alphey, M.S., (1999) J. Struct. Biol., 126, 76. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. obs: 35022 / % possible obs: 96.6 % / Redundancy: 2 % / Biso Wilson estimate: 14.4 Å2 / Rsym value: 0.045 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.439 / % possible all: 88.9 |
Reflection | *PLUS Redundancy: 7.5 % / Num. measured all: 261452 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS % possible obs: 88.9 % / Rmerge(I) obs: 0.439 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QK8 Resolution: 1.3→28.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.926 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→28.99 Å
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Refine LS restraints |
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