+Open data
-Basic information
Entry | Database: PDB / ID: 7kj0 | ||||||
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Title | hyperoxidized human peroxiredoxin 2 | ||||||
Components | Peroxiredoxin-2 | ||||||
Keywords | OXIDOREDUCTASE / hydrogen peroxide | ||||||
Function / homology | Function and homology information respiratory burst involved in inflammatory response / leukocyte activation / negative regulation of T cell differentiation / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species ...respiratory burst involved in inflammatory response / leukocyte activation / negative regulation of T cell differentiation / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / T cell homeostasis / antioxidant activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of blood coagulation / T cell proliferation / extrinsic apoptotic signaling pathway / removal of superoxide radicals / cell redox homeostasis / thymus development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / cellular response to oxidative stress / regulation of apoptotic process / response to oxidative stress / response to lipopolysaccharide / positive regulation of MAPK cascade / negative regulation of apoptotic process / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Kean, K.M. / Karplus, P.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Modifying the resolving cysteine affects the structure and hydrogen peroxide reactivity of peroxiredoxin 2. Authors: Peskin, A.V. / Meotti, F.C. / Kean, K.M. / Gobl, C. / Peixoto, A.S. / Pace, P.E. / Horne, C.R. / Heath, S.G. / Crowther, J.M. / Dobson, R.C.J. / Karplus, P.A. / Winterbourn, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kj0.cif.gz | 945.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kj0.ent.gz | 644.7 KB | Display | PDB format |
PDBx/mmJSON format | 7kj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/7kj0 ftp://data.pdbj.org/pub/pdb/validation_reports/kj/7kj0 | HTTPS FTP |
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-Related structure data
Related structure data | 7kizSC 7kj1C 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: 21819.691 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX2, NKEFB, TDPX1 / Production host: Escherichia coli (E. coli) References: UniProt: P32119, thioredoxin-dependent peroxiredoxin #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.88 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 25% PEG 3350, 0.2 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→49.6 Å / Num. obs: 109799 / % possible obs: 97.9 % / Redundancy: 22.5 % / Biso Wilson estimate: 45.91 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.461 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.29→2.35 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 8119 / CC1/2: 0.318 / Rrim(I) all: 5.327 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KIZ Resolution: 2.29→49.6 Å / SU ML: 0.3535 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.0373 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→49.6 Å
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Refine LS restraints |
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LS refinement shell |
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