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- PDB-3tkr: Crystal structure of full-length human peroxiredoxin 4 with T118E... -

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Basic information

Entry
Database: PDB / ID: 3tkr
TitleCrystal structure of full-length human peroxiredoxin 4 with T118E mutation
ComponentsPeroxiredoxin-4
KeywordsOXIDOREDUCTASE / Trx fold / peroxiredoxin
Function / homology
Function and homology information


: / negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / molecular sequestering activity / 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 / thioredoxin peroxidase activity / molecular sequestering activity / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / secretory granule lumen / spermatogenesis / molecular adaptor activity / response to oxidative stress / ficolin-1-rich granule lumen / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol
Similarity search - Function
: / 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, 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWang, X. / Wang, L. / Wang, X. / Sun, F. / Wang, C.-C.
CitationJournal: 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
DepositionAug 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / 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-4
I: Peroxiredoxin-4
G: Peroxiredoxin-4
C: Peroxiredoxin-4
F: Peroxiredoxin-4
D: Peroxiredoxin-4
B: Peroxiredoxin-4
H: Peroxiredoxin-4
E: Peroxiredoxin-4
J: Peroxiredoxin-4


Theoretical massNumber of molelcules
Total (without water)280,39610
Polymers280,39610
Non-polymers00
Water38,4622135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30010 Å2
ΔGint-194 kcal/mol
Surface area72230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.710, 139.117, 178.970
Angle α, β, γ (deg.)90.00, 96.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peroxiredoxin-4 / Antioxidant enzyme AOE372 / AOE37-2 / Peroxiredoxin IV / Prx-IV / Thioredoxin peroxidase AO372 / ...Antioxidant enzyme AOE372 / AOE37-2 / Peroxiredoxin IV / Prx-IV / Thioredoxin peroxidase AO372 / Thioredoxin-dependent peroxide reductase A0372


Mass: 28039.615 Da / Num. of mol.: 10 / Mutation: T118E
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2135 / 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: 2.72 Å3/Da / Density % sol: 54.83 % / Mosaicity: 0.338 °
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 174367 / Num. obs: 171228 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.054 / Χ2: 1.675 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.20.183145870.555183.8
2.18-2.263.70.169171410.573198.7
2.26-2.373.90.136173600.61199.7
2.37-2.493.90.114173660.648199.8
2.49-2.653.90.091173330.679199.9
2.65-2.853.90.074174130.7751100
2.85-3.143.90.054174080.9381100
3.14-3.593.90.039174701.3721100
3.59-4.523.90.031174952.1871100
4.52-503.80.035176557.924199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PN8

2pn8


Resolution: 2.1→46.004 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8972 / SU ML: 0.24 / σ(F): 0 / Phase error: 17.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 8351 4.99 %Random
Rwork0.1502 ---
obs0.1516 167350 95.83 %-
all-174367 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.525 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 83.9 Å2 / Biso mean: 22.9176 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1-7.2792 Å2-0 Å23.9322 Å2
2---3.3136 Å20 Å2
3----3.9656 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15802 0 0 2135 17937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716366
X-RAY DIFFRACTIONf_angle_d1.04822248
X-RAY DIFFRACTIONf_chiral_restr0.0752426
X-RAY DIFFRACTIONf_plane_restr0.0052874
X-RAY DIFFRACTIONf_dihedral_angle_d12.1786085
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.17520.20256670.1625128451351278
2.1752-2.26220.20677890.1609155471633694
2.2622-2.36520.20488330.1566159351676896
2.3652-2.48990.1928260.1539161071693397
2.4899-2.64590.18718740.1496161291700398
2.6459-2.85010.19018960.1545162481714498
2.8501-3.13690.18498880.1567164091729799
3.1369-3.59070.17268680.1479165101737899
3.5907-4.52320.14858520.13181661517467100
4.5232-46.01540.16888580.1558166541751299

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