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Yorodumi- PDB-3tks: Crystal structure of full-length human peroxiredoxin 4 in three d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tks | ||||||
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Title | Crystal structure of full-length human peroxiredoxin 4 in three different redox states | ||||||
Components | (Peroxiredoxin-4) x 3 | ||||||
Keywords | OXIDOREDUCTASE / Trx fold / peroxiredoxin | ||||||
Function / homology | Function and homology information 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 ...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 / response to oxidative stress / ficolin-1-rich granule lumen / molecular adaptor activity / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wang, X. / Wang, L. / Wang, X. / Sun, F. / Wang, C.-C. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Structural insights into the peroxidase activity and inactivation of human peroxiredoxin 4 Authors: Wang, X. / Wang, L. / Wang, X. / Sun, F. / Wang, C.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tks.cif.gz | 219.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tks.ent.gz | 173.9 KB | Display | PDB format |
PDBx/mmJSON format | 3tks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tks_validation.pdf.gz | 486.1 KB | Display | wwPDB validaton report |
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Full document | 3tks_full_validation.pdf.gz | 502.2 KB | Display | |
Data in XML | 3tks_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 3tks_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/3tks ftp://data.pdbj.org/pub/pdb/validation_reports/tk/3tks | HTTPS FTP |
-Related structure data
Related structure data | 3tkpC 3tkqC 3tkrC 2pn8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28027.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX4 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q13162, peroxiredoxin #2: Protein | Mass: 28043.604 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX4 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q13162, peroxiredoxin #3: Protein | | Mass: 28011.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX4 / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q13162, peroxiredoxin #4: Chemical | #5: 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: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.8M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 5mM DTT, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 13, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. all: 59098 / Num. obs: 57443 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.085 / Χ2: 0.935 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PN8 Resolution: 2.4→30.523 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8287 / SU ML: 0.32 / σ(F): 0 / Phase error: 24.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.85 Å2 / Biso mean: 39.0616 Å2 / Biso min: 13.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30.523 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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