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- PDB-7kj1: human peroxiredoxin 2 - C172S mutant -

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Basic information

Entry
Database: PDB / ID: 7kj1
Titlehuman peroxiredoxin 2 - C172S mutant
ComponentsPeroxiredoxin-2
KeywordsOXIDOREDUCTASE / hydrogen peroxide
Function / homology
Function and homology information


respiratory burst involved in inflammatory response / negative regulation of T cell differentiation / leukocyte activation / regulation of hydrogen peroxide metabolic process / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin-dependent peroxiredoxin / 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 / negative regulation of T cell differentiation / leukocyte activation / regulation of hydrogen peroxide metabolic process / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin-dependent peroxiredoxin / 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: 2.15 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)217,71610
Polymers217,71610
Non-polymers00
Water31,5801753
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28270 Å2
ΔGint-180 kcal/mol
Surface area70680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.200, 88.300, 125.200
Angle α, β, γ (deg.)90.000, 99.200, 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: 21771.627 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


Mass: 18.015 Da / Num. of mol.: 1753 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.91 %
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: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→35.24 Å / Num. obs: 136298 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 43.51 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.252 / Net I/σ(I): 7.5
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 10028 / CC1/2: 0.195 / Rrim(I) all: 2.825 / % possible all: 99.9

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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

7kiz


Resolution: 2.15→35.24 Å / SU ML: 0.3948 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2365 6706 4.98 %
Rwork0.195 128025 -
obs0.1971 134731 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.63 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15378 0 0 1753 17131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001816309
X-RAY DIFFRACTIONf_angle_d0.490822170
X-RAY DIFFRACTIONf_chiral_restr0.04372421
X-RAY DIFFRACTIONf_plane_restr0.00292930
X-RAY DIFFRACTIONf_dihedral_angle_d17.47666040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.40552060.39194105X-RAY DIFFRACTION96.38
2.17-2.20.40222210.37434344X-RAY DIFFRACTION99.89
2.2-2.230.39762270.3794274X-RAY DIFFRACTION99.91
2.23-2.250.56811930.52883628X-RAY DIFFRACTION83.85
2.25-2.280.46971770.44413524X-RAY DIFFRACTION81.99
2.28-2.320.37182440.33954280X-RAY DIFFRACTION99.93
2.32-2.350.34782220.3194303X-RAY DIFFRACTION99.93
2.35-2.380.33372310.29784306X-RAY DIFFRACTION99.82
2.38-2.420.32962200.29924271X-RAY DIFFRACTION99.76
2.42-2.460.33112270.27984364X-RAY DIFFRACTION99.83
2.46-2.50.29282180.26614296X-RAY DIFFRACTION99.93
2.5-2.550.30132350.2584336X-RAY DIFFRACTION99.96
2.55-2.60.31392340.25274297X-RAY DIFFRACTION99.85
2.6-2.650.29222190.25464235X-RAY DIFFRACTION99.58
2.65-2.710.34562190.26614347X-RAY DIFFRACTION99.78
2.71-2.770.32782280.23994310X-RAY DIFFRACTION99.87
2.77-2.840.25012260.22454324X-RAY DIFFRACTION99.89
2.84-2.920.27642340.22024284X-RAY DIFFRACTION99.91
2.92-30.25171980.20414338X-RAY DIFFRACTION99.89
3-3.10.24312380.1974287X-RAY DIFFRACTION99.98
3.1-3.210.23812290.20334349X-RAY DIFFRACTION99.96
3.21-3.340.23752240.17774305X-RAY DIFFRACTION99.93
3.34-3.490.20842420.16474333X-RAY DIFFRACTION99.87
3.49-3.670.20642350.15664343X-RAY DIFFRACTION99.83
3.67-3.90.192230.14934327X-RAY DIFFRACTION99.82
3.9-4.20.19272350.13584332X-RAY DIFFRACTION99.89
4.2-4.630.14832190.11494374X-RAY DIFFRACTION99.93
4.63-5.290.14812150.12064354X-RAY DIFFRACTION99.96
5.29-6.660.20632250.15954408X-RAY DIFFRACTION99.94
6.66-35.240.21012420.18434447X-RAY DIFFRACTION99.51

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