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- PDB-3tjg: Crystal Structure of human peroxiredoxin IV C51A mutant in oxidiz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tjg | ||||||
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Title | Crystal Structure of human peroxiredoxin IV C51A mutant in oxidized form | ||||||
![]() | Peroxiredoxin-4 | ||||||
![]() | OXIDOREDUCTASE / thioredoxin fold / sulfenylation / endoplasmic reticulum | ||||||
Function / homology | ![]() cellular response to stress / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process ...cellular response to stress / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / spermatogenesis / secretory granule lumen / ficolin-1-rich granule lumen / response to oxidative stress / molecular adaptor activity / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, Z. / Tavender, T.J. / Roszak, A.W. / Cogdell, R.J. / Bulleid, N.J. | ||||||
![]() | ![]() Title: Crystal Structure of Reduced and of Oxidized Peroxiredoxin IV Enzyme Reveals a Stable Oxidized Decamer and a Non-disulfide-bonded Intermediate in the Catalytic Cycle. Authors: Cao, Z. / Tavender, T.J. / Roszak, A.W. / Cogdell, R.J. / Bulleid, N.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 396.5 KB | Display | ![]() |
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PDB format | ![]() | 327.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.5 KB | Display | ![]() |
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Full document | ![]() | 490.8 KB | Display | |
Data in XML | ![]() | 40.8 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tjbC ![]() 3tjfC ![]() 3tjjC ![]() 3tjkC ![]() 2pn8S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28803.428 Da / Num. of mol.: 5 / Fragment: UNP residues 38-271 / Mutation: C51A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 48% PEG200, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2010 / Details: mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→28.96 Å / Num. all: 64808 / Num. obs: 64808 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.24→2.3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4733 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PN8 Resolution: 2.24→28.96 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 10.99 / SU ML: 0.119 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.929 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→28.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.302 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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