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Open data
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Basic information
Entry | Database: PDB / ID: 1e2y | ||||||
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Title | Tryparedoxin peroxidase from Crithidia fasciculata | ||||||
![]() | TRYPAREDOXIN PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / 2-CYS PEROXIREDOXIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alphey, M.S. / Bond, C.S. / Hunter, W.N. | ||||||
![]() | ![]() Title: The Structure of Reduced Tryparedoxin Peroxidase Reveals a Decamer and Insight Into Reactivity of 2Cys-Peroxiredoxins Authors: Alphey, M.S. / Bond, C.S. / 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 | ![]() | 315.9 KB | Display | ![]() |
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PDB format | ![]() | 271.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 526.8 KB | Display | ![]() |
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Full document | ![]() | 625.8 KB | Display | |
Data in XML | ![]() | 70.1 KB | Display | |
Data in CIF | ![]() | 92.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 21313.393 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: PLASMID TRANSFORMED INTO E. COLI BL21(DE3) STRAIN FOR RECOMBINANT PROTEIN EXPRESSION Cellular location: CYTOPLASM / Gene: CF-TRYP / Production host: ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: PROTEIN CRYSTALLIZED FROM 12.5% PEG 1000, 100MM TRIS-HCL PH HANGING DROP CONSISITED | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of 2.5 micro litter of protein mixed with 2 micro litter of reservoir solution and 0.5 micro litter EDTA | ||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999 / Details: MIRROR | ||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→21 Å / Num. obs: 52094 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 56.4 Å2 / Rsym value: 0.091 / Net I/σ(I): 14.8 | ||||||||||||
Reflection shell | Resolution: 3.2→21 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.48 / % possible all: 96.7 | ||||||||||||
Reflection | *PLUS Num. measured all: 376643 / Rmerge(I) obs: 0.091 | ||||||||||||
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.48 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: DENSITY MODIFICATION / Bsol: 12.362 Å2 / ksol: 0.205 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→21 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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