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- PDB-3vwu: Crystal structure of peroxiredoxin 4 from M. musculus -

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Basic information

Entry
Database: PDB / ID: 3vwu
TitleCrystal structure of peroxiredoxin 4 from M. musculus
ComponentsPeroxiredoxin-4
KeywordsOXIDOREDUCTASE / peroxiredoxin family / thioredoxin fold / peroxiredoxin
Function / homology
Function and homology information


cellular response to stress / negative regulation of male germ cell proliferation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding / smooth endoplasmic reticulum / Neutrophil degranulation / reactive oxygen species metabolic process / extracellular matrix organization ...cellular response to stress / negative regulation of male germ cell proliferation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / protein maturation by protein folding / smooth endoplasmic reticulum / Neutrophil degranulation / reactive oxygen species metabolic process / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / spermatogenesis / response to oxidative stress / endoplasmic reticulum / mitochondrion / extracellular space / identical protein binding / cytoplasm / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsInaba, K. / Suzuki, M.
CitationJournal: Sci Rep / Year: 2013
Title: Synergistic cooperation of PDI family members in peroxiredoxin 4-driven oxidative protein folding
Authors: Sato, Y. / Kojima, R. / Okumura, M. / Hagiwara, M. / Masui, S. / Maegawa, K. / Saiki, M. / Horibe, T. / Suzuki, M. / Inaba, K.
History
DepositionSep 3, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin-4
B: Peroxiredoxin-4
C: Peroxiredoxin-4
D: Peroxiredoxin-4
E: Peroxiredoxin-4
F: Peroxiredoxin-4
G: Peroxiredoxin-4
H: Peroxiredoxin-4
I: Peroxiredoxin-4
J: Peroxiredoxin-4


Theoretical massNumber of molelcules
Total (without water)287,80510
Polymers287,80510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19460 Å2
ΔGint-144 kcal/mol
Surface area68220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.468, 118.656, 255.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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


Mass: 28780.486 Da / Num. of mol.: 10 / Mutation: C54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prdx4 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08807, 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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 8-10% PEG-MME 550, 50mM MES, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 15, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→43.73 Å / Num. obs: 38676 / % possible obs: 94.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 69.36 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.9
Reflection shellResolution: 3.3→3.38 Å / % possible all: 88.7

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→43.108 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8335 / SU ML: 0.36 / σ(F): 1.41 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 1936 5.01 %random
Rwork0.2027 ---
obs0.2054 38605 94.41 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.345 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso max: 164.07 Å2 / Biso mean: 67.0966 Å2 / Biso min: 29.25 Å2
Baniso -1Baniso -2Baniso -3
1--5.1922 Å2-0 Å20 Å2
2--8.5102 Å20 Å2
3----3.3179 Å2
Refinement stepCycle: LAST / Resolution: 3.3→43.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13617 0 0 0 13617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413960
X-RAY DIFFRACTIONf_angle_d1.74818926
X-RAY DIFFRACTIONf_dihedral_angle_d14.7155100
X-RAY DIFFRACTIONf_chiral_restr0.0922099
X-RAY DIFFRACTIONf_plane_restr0.012420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.38250.26621260.2166240688
3.3825-3.47390.31151010.2253244089
3.4739-3.57610.26781450.2303239588
3.5761-3.69150.29681400.2203242389
3.6915-3.82330.25861410.2133243789
3.8233-3.97630.2721400.205250391
3.9763-4.15710.24211360.1889254693
4.1571-4.37610.23731350.1762264896
4.3761-4.650.21761340.169271899
4.65-5.00850.1981240.1742781100
5.0085-5.51160.31131590.21792771100
5.5116-6.3070.28341350.21592820100
6.307-7.93810.24951480.19122846100
7.9381-43.11150.23751720.2222293599

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