+Open data
-Basic information
Entry | Database: PDB / ID: 1e2y | ||||||
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Title | Tryparedoxin peroxidase from Crithidia fasciculata | ||||||
Components | TRYPAREDOXIN PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / 2-CYS PEROXIREDOXIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CRITHIDIA FASCICULATA (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å | ||||||
Authors | Alphey, M.S. / Bond, C.S. / Hunter, W.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e2y.cif.gz | 315.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e2y.ent.gz | 271.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e2y_validation.pdf.gz | 526.8 KB | Display | wwPDB validaton report |
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Full document | 1e2y_full_validation.pdf.gz | 625.8 KB | Display | |
Data in XML | 1e2y_validation.xml.gz | 70.1 KB | Display | |
Data in CIF | 1e2y_validation.cif.gz | 92.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2y ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2y | 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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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.) CRITHIDIA FASCICULATA (eukaryote) Description: PLASMID TRANSFORMED INTO E. COLI BL21(DE3) STRAIN FOR RECOMBINANT PROTEIN EXPRESSION Cellular location: CYTOPLASM / Gene: CF-TRYP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9TZX2 #2: Chemical | ChemComp-CL / #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: 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8800,0.9790,0.9792 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→21 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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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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