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- PDB-5ykj: Structural basis of the thiol resolving mechanism in yeast mitoch... -

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Basic information

Entry
Database: PDB / ID: 5ykj
TitleStructural basis of the thiol resolving mechanism in yeast mitochondrial 1-Cys peroxiredoxin via glutathione/thioredoxin systems
ComponentsPeroxiredoxin PRX1, mitochondrial
KeywordsTRANSFERASE / Saccharomyces cerevisiae / 1-Cys Peroxiredoxin / Thioredoxin / glutathione
Function / homology
Function and homology information


: / glutaredoxin-dependent peroxiredoxin / glutathione-dependent peroxiredoxin / thioredoxin peroxidase activity / response to cadmium ion / Neutrophil degranulation / cell redox homeostasis / peroxidase activity / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 1-Cys peroxiredoxin / 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 ...Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 1-Cys peroxiredoxin / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peroxiredoxin PRX1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 Å
AuthorsLi, C.C. / Yang, J. / Yang, M.J. / Liu, L. / Peng, C.T. / Li, T. / He, L.H. / Song, Y.J. / Zhu, Y.B. / Zhao, N.L. ...Li, C.C. / Yang, J. / Yang, M.J. / Liu, L. / Peng, C.T. / Li, T. / He, L.H. / Song, Y.J. / Zhu, Y.B. / Zhao, N.L. / Zhao, C. / Bao, R.
CitationJournal: To be published
Title: Structural basis of the thiol resolving mechanism in yeast mitochondrial 1-Cys peroxiredoxin via glutathione/thioredoxin systems
Authors: Li, C.C. / Yang, J. / Yang, M.J. / Liu, L. / Peng, C.T. / Li, T. / He, L.H. / Song, Y.J. / Zhu, Y.B. / Zhao, N.L. / Zhao, C. / Bao, R.
History
DepositionOct 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev / _citation.unpublished_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin PRX1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2723
Polymers24,1571
Non-polymers1152
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-9 kcal/mol
Surface area10960 Å2
Unit cell
Length a, b, c (Å)84.030, 84.030, 62.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-591-

HOH

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Components

#1: Protein Peroxiredoxin PRX1, mitochondrial / Prx / 1-Cys PRX / Mitochondrial thiol peroxidase / mTPx / Thioredoxin peroxidase


Mass: 24156.521 Da / Num. of mol.: 1 / Fragment: UNP residues 49-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PRX1, YBL064C, YBL0503, YBL0524 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34227, peroxiredoxin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.3 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 23% (W/V) PEG-2000 MME ,100mM Tris base/Hydrochloric acid pH 4.7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97022 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97022 Å / Relative weight: 1
ReflectionResolution: 1.53→43.2 Å / Num. obs: 34456 / % possible obs: 99.99 % / Redundancy: 22.5 % / Rsym value: 0.161 / Net I/σ(I): 14.24
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 18.3 % / Mean I/σ(I) obs: 3.87 / Num. unique obs: 3385 / Rsym value: 0.739 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.53→43.156 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 17.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 2000 5.81 %
Rwork0.1784 --
obs0.1793 34452 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→43.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 7 229 1932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0311756
X-RAY DIFFRACTIONf_angle_d1.9822384
X-RAY DIFFRACTIONf_dihedral_angle_d19.093650
X-RAY DIFFRACTIONf_chiral_restr0.154269
X-RAY DIFFRACTIONf_plane_restr0.009307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5303-1.56860.32951400.3192274X-RAY DIFFRACTION100
1.5686-1.6110.29591410.2962274X-RAY DIFFRACTION100
1.611-1.65840.26941380.28142265X-RAY DIFFRACTION100
1.6584-1.71190.30911410.25582285X-RAY DIFFRACTION100
1.7119-1.77310.26831420.23692292X-RAY DIFFRACTION100
1.7731-1.84410.25041410.21292292X-RAY DIFFRACTION100
1.8441-1.9280.22511410.18022282X-RAY DIFFRACTION100
1.928-2.02970.17221410.15772301X-RAY DIFFRACTION100
2.0297-2.15690.19151430.15352314X-RAY DIFFRACTION100
2.1569-2.32340.15181430.14022320X-RAY DIFFRACTION100
2.3234-2.55720.14791440.14142325X-RAY DIFFRACTION100
2.5572-2.92710.1821430.1482341X-RAY DIFFRACTION100
2.9271-3.68760.15491480.14482382X-RAY DIFFRACTION100
3.6876-43.1730.16231540.16852505X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.629-0.005-0.24660.6487-0.05060.7104-0.0306-0.0696-0.08660.0031-0.0117-0.08350.12870.0440.0330.09910.0114-0.00580.07460.01960.09725.50758.36359.6176
21.20010.9753-0.40712.5044-0.52411.02790.0337-0.2142-0.08360.152-0.12030.08090.07670.0810.05690.10570.025600.1350.02770.112222.56967.456621.2037
31.681-0.16940.36622.05870.01971.3934-0.0572-0.33070.16340.2345-0.06350.1594-0.28180.00630.09180.1077-0.0184-0.00330.1355-0.00930.127228.038924.046813.7271
40.5252-0.20780.28290.4258-0.04551.00480.04340.0667-0.0495-0.0706-0.0334-0.01570.19050.0405-0.00090.11420.00190.01580.0666-0.00460.084518.73397.5114-6.1109
52.8447-0.6974-0.31783.2439-0.30271.53860.06470.1493-0.17260.0917-0.01020.0490.3793-0.0064-0.09530.17850.0325-0.01160.0929-0.0420.113112.16113.1524-24.297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 169 )
4X-RAY DIFFRACTION4chain 'A' and (resid 170 through 245 )
5X-RAY DIFFRACTION5chain 'A' and (resid 246 through 260 )

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