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- PDB-2z9s: Crystal Structure Analysis of rat HBP23/Peroxiredoxin I, Cys52Ser... -

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Basic information

Entry
Database: PDB / ID: 2z9s
TitleCrystal Structure Analysis of rat HBP23/Peroxiredoxin I, Cys52Ser mutant
ComponentsPeroxiredoxin-1
KeywordsOXIDOREDUCTASE / peroxiredoxin / 2-Cys type peroxiredoxin / decamer / thiol-specific antioxidant protein / HBP23 / Cytoplasm / Peroxidase / Phosphorylation / Redox-active center
Function / homology
Function and homology information


NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / leukocyte activation / TP53 Regulates Metabolic Genes / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / natural killer cell mediated cytotoxicity / thioredoxin peroxidase activity / natural killer cell activation ...NFE2L2 regulating anti-oxidant/detoxification enzymes / Detoxification of Reactive Oxygen Species / leukocyte activation / TP53 Regulates Metabolic Genes / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / natural killer cell mediated cytotoxicity / thioredoxin peroxidase activity / natural killer cell activation / erythrocyte homeostasis / regulation of stress-activated MAPK cascade / peroxisomal matrix / canonical NF-kappaB signal transduction / removal of superoxide radicals / cell redox homeostasis / response to reactive oxygen species / hydrogen peroxide catabolic process / euchromatin / peroxidase activity / fibroblast proliferation / response to oxidative stress / mitochondrial matrix / heme binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMatsumura, T. / Okamoto, K. / Nishino, T. / Abe, Y.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Dimer-Oligomer Interconversion of Wild-type and Mutant Rat 2-Cys Peroxiredoxin: DISULFIDE FORMATION AT DIMER-DIMER INTERFACES IS NOT ESSENTIAL FOR DECAMERIZATION
Authors: Matsumura, T. / Okamoto, K. / Iwahara, S. / Hori, H. / Takahashi, Y. / Nishino, T. / Abe, Y.
#1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1999
Title: Crystal structure of a multifunctional 2-Cys peroxiredoxin heme-binding protein 23 kDa/proliferation-associated gene product
Authors: Hirotsu, S. / Abe, Y. / Okada, K. / Nagahara, N. / Hori, H. / Nishino, T. / Hakoshima, T.
History
DepositionSep 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin-1
B: Peroxiredoxin-1
C: Peroxiredoxin-1
D: Peroxiredoxin-1
E: Peroxiredoxin-1
F: Peroxiredoxin-1
G: Peroxiredoxin-1
H: Peroxiredoxin-1
I: Peroxiredoxin-1
J: Peroxiredoxin-1


Theoretical massNumber of molelcules
Total (without water)221,22310
Polymers221,22310
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.312, 111.637, 120.740
Angle α, β, γ (deg.)90.00, 112.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peroxiredoxin-1 / Thioredoxin peroxidase 2 / Thioredoxin-dependent peroxide reductase 2 / Heme-binding 23 kDa protein / HBP23


Mass: 22122.338 Da / Num. of mol.: 10 / Mutation: C52S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prdx1, Tdpx2 / Plasmid: pET3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q63716, peroxiredoxin

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: pH5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 48708

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å
RfactorNum. reflection
Rfree0.269 2532
Rwork0.205 -
obs-48708
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15460 0 0 0 15460

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