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- PDB-7kj0: hyperoxidized human peroxiredoxin 2 -

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Basic information

Entry
Database: PDB / ID: 7kj0
Titlehyperoxidized human peroxiredoxin 2
ComponentsPeroxiredoxin-2
KeywordsOXIDOREDUCTASE / 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
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKean, K.M. / Karplus, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM119227 United States
CitationJournal: 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
DepositionOct 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin-2
B: Peroxiredoxin-2
C: Peroxiredoxin-2
D: Peroxiredoxin-2
E: Peroxiredoxin-2
F: Peroxiredoxin-2
G: Peroxiredoxin-2
H: Peroxiredoxin-2
I: Peroxiredoxin-2
J: Peroxiredoxin-2


Theoretical massNumber of molelcules
Total (without water)218,19710
Polymers218,19710
Non-polymers00
Water31,3101738
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28300 Å2
ΔGint-193 kcal/mol
Surface area70930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.000, 88.000, 125.600
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Peroxiredoxin-2 / / Natural killer cell-enhancing factor B / NKEF-B / PRP / Thiol-specific antioxidant protein / TSA / ...Natural killer cell-enhancing factor B / NKEF-B / PRP / Thiol-specific antioxidant protein / TSA / Thioredoxin peroxidase 1 / Thioredoxin-dependent peroxide reductase 1 / Thioredoxin-dependent peroxiredoxin 2


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 1738 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 25% PEG 3350, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2329 5447 4.96 %
Rwork0.1823 104286 -
obs0.1849 109733 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.02 Å2
Refinement stepCycle: LAST / Resolution: 2.29→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15398 0 0 1738 17136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002116331
X-RAY DIFFRACTIONf_angle_d0.57122203
X-RAY DIFFRACTIONf_chiral_restr0.04492421
X-RAY DIFFRACTIONf_plane_restr0.0042931
X-RAY DIFFRACTIONf_dihedral_angle_d18.43496041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.310.39161780.3593384X-RAY DIFFRACTION96.4
2.31-2.340.36881980.31873507X-RAY DIFFRACTION99.97
2.34-2.370.35121810.30233559X-RAY DIFFRACTION100
2.37-2.40.31571680.29043530X-RAY DIFFRACTION99.95
2.4-2.430.31421880.29113554X-RAY DIFFRACTION99.95
2.43-2.460.32641860.27323528X-RAY DIFFRACTION99.95
2.46-2.50.28571890.26093504X-RAY DIFFRACTION100
2.5-2.540.29911810.25163540X-RAY DIFFRACTION99.97
2.54-2.580.31962030.25343532X-RAY DIFFRACTION99.97
2.58-2.620.27941720.26033528X-RAY DIFFRACTION99.95
2.62-2.660.30761910.26083545X-RAY DIFFRACTION99.89
2.66-2.710.32281690.25633524X-RAY DIFFRACTION99.89
2.71-2.760.33411890.23483534X-RAY DIFFRACTION100
2.76-2.820.29421940.23173537X-RAY DIFFRACTION99.95
2.82-2.880.30091730.22513559X-RAY DIFFRACTION100
2.88-2.950.28821840.21743556X-RAY DIFFRACTION100
2.95-3.020.25511690.19823561X-RAY DIFFRACTION99.97
3.02-3.10.25991990.19093504X-RAY DIFFRACTION99.97
3.1-3.190.25521820.19163553X-RAY DIFFRACTION99.97
3.19-3.30.25241840.18523543X-RAY DIFFRACTION100
3.3-3.420.2172010.16423544X-RAY DIFFRACTION100
3.42-3.550.21341930.15733546X-RAY DIFFRACTION99.92
3.55-3.710.22791250.16022384X-RAY DIFFRACTION67.25
3.71-3.890.21191660.15013158X-RAY DIFFRACTION97.34
3.94-4.150.17461660.13493026X-RAY DIFFRACTION99.72
4.15-4.480.17011560.11533578X-RAY DIFFRACTION100
4.48-4.930.151980.11223580X-RAY DIFFRACTION99.97
4.93-5.640.18591840.13923599X-RAY DIFFRACTION100
5.64-7.10.22321850.17333591X-RAY DIFFRACTION100
7.1-49.60.21131950.18423698X-RAY DIFFRACTION99.74

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