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- PDB-5ept: Crystal Structure of S. cerevisiae TSA2 in the disulfide state -

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Basic information

Entry
Database: PDB / ID: 5ept
TitleCrystal Structure of S. cerevisiae TSA2 in the disulfide state
ComponentsPeroxiredoxin TSA2
KeywordsOXIDOREDUCTASE / Peroxiredoxin / Peroxidase / Oxidative Stress
Function / homology
Function and homology information


NFE2L2 regulating anti-oxidant/detoxification enzymes / TP53 Regulates Metabolic Genes / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / peroxiredoxin activity / cell redox homeostasis / hydrogen peroxide catabolic process / protein folding / cellular response to oxidative stress / response to oxidative stress ...NFE2L2 regulating anti-oxidant/detoxification enzymes / TP53 Regulates Metabolic Genes / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / peroxiredoxin activity / cell redox homeostasis / hydrogen peroxide catabolic process / protein folding / cellular response to oxidative stress / response to oxidative stress / protein stabilization / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsNielsen, M.H. / Kidmose, R.T. / Jenner, L.B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structure of TSA2 reveals novel features of the active-site loop of peroxiredoxins.
Authors: Nielsen, M.H. / Kidmose, R.T. / Jenner, L.B.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3Jan 10, 2024Group: 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
H: Peroxiredoxin TSA2
B: Peroxiredoxin TSA2
C: Peroxiredoxin TSA2
A: Peroxiredoxin TSA2
G: Peroxiredoxin TSA2
I: Peroxiredoxin TSA2
D: Peroxiredoxin TSA2
E: Peroxiredoxin TSA2
J: Peroxiredoxin TSA2
F: Peroxiredoxin TSA2


Theoretical massNumber of molelcules
Total (without water)242,12510
Polymers242,12510
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17520 Å2
ΔGint-94 kcal/mol
Surface area77480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.460, 167.210, 221.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peroxiredoxin TSA2 / Cytoplasmic thiol peroxidase 2 / cTPx 2 / Thiol-specific antioxidant protein 2 / Thioredoxin peroxidase 2


Mass: 24212.541 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TSA2, YDR453C, D9461.38 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04120, 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: 3.92 Å3/Da / Density % sol: 68.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 6% (w/v) PEG20K, 0.2 M MgCl2, 0.1M NaCitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 5→46.4 Å / Num. obs: 13476 / % possible obs: 50.6 % / Observed criterion σ(I): -3 / Redundancy: 20 % / Biso Wilson estimate: 195.25 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 13.98 / Num. measured all: 13476
Reflection shell
Resolution (Å)Num. measured obsNum. possibleNum. unique obsDiffraction-IDRejects% possible all
5-5.2391897391099.9
4.12-4.2493189793104.9
4.24-4.361591855159108.6
4.36-4.4922017652201012.5
4.49-4.6430117753011017
4.64-4.838216473821023.2
4.8-4.9848816204881030.1
4.98-5.1965115846511041.1
5.19-5.4284614928461056.7
5.42-5.681005145810051068.9
5.68-5.991109137011091080.9
5.99-6.351222129812221094.1
6.35-6.7912311231123110100
6.79-7.3411541154115410100
7.34-8.0410661066106610100
8.04-8.9896496496410100
8.98-10.3788788788710100
10.37-12.7172772772710100
12.71-17.9759259259210100
17.97-46.43403623401093.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DVB

5dvb


Resolution: 5→46.351 Å / SU ML: 0.79 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 48.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3748 1171 10.04 %
Rwork0.2737 10488 -
obs0.284 11659 83.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 609.03 Å2 / Biso mean: 350.0008 Å2 / Biso min: 214.05 Å2
Refinement stepCycle: final / Resolution: 5→46.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13616 0 0 0 13616
Num. residues----1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713924
X-RAY DIFFRACTIONf_angle_d1.12918869
X-RAY DIFFRACTIONf_chiral_restr0.0662128
X-RAY DIFFRACTIONf_plane_restr0.0082414
X-RAY DIFFRACTIONf_dihedral_angle_d14.1328498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.0002-5.22750.4004740.322666473843
5.2275-5.50270.48171020.3087915101760
5.5027-5.84680.43031290.3381148127774
5.8468-6.29720.41471550.36011377153289
6.2972-6.92910.42131740.334315641738100
6.9291-7.92740.41181740.33461563173799
7.9274-9.97130.33471760.257815791755100
9.9713-46.35290.35371870.22691678186599
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)
13.17791.3119-3.30971.4661-0.00244.6113-0.1562.6491-0.0727-0.39150.41530.5661-3.3058-3.28440.73050.1905-0.1320.38476.3022-0.54673.607249.3539-39.3019-20.519
22.1368-2.7292-0.9559.01757.33866.88221.9777-2.1178-0.01324.34520.34721.96721.75741.56920.9954-1.2105-1.94922.05332.260.37492.823764.1102-43.6059-20.8484
38.10631.9665-4.59132.25182.29139.2654-0.2436-2.34393.6764-0.17340.29572.04610.12153.3368-0.22624.02180.31880.21393.67630.16263.473470.7755-49.1798-25.8789
43.5798-1.6926-0.42594.9663-1.58082.9805-2.2094-0.8923-0.36580.81690.4841-0.5491-2.4663-2.34290.89682.844-0.3671-0.35473.05610.47752.889157.8064-33.3919-17.5088
54.7878-4.4653-2.97274.77581.78665.3556-1.4171-2.3796-3.5031-1.21531.13321.92443.59463.32861.15244.79941.8438-1.29254.32080.36383.816253.7809-45.1393-1.9889
65.09565.06491.32987.02331.07051.3827-2.46882.79014.66541.57571.6587-1.78022.48922.84081.21314.34462.1054-0.43786.1018-0.40022.873553.3952-44.40227.6378
76.72111.3799-4.59073.0372.37236.2764-0.8472-3.291-1.01473.4859-1.875-2.72260.30541.40561.32743.80580.04330.22252.5360.48253.638712.60119.8574-51.6475
88.91943.1227-4.10447.74492.90836.5134-0.29410.01360.1879-1.09861.79742.22490.3288-0.16720.33522.94770.4625-1.32913.85430.64174.084512.638318.3544-60.986
93.2353-2.61774.15182.4737-3.84726.0033-4.0999-10.58881.82097.04312.18970.6742-8.70142.22491.2747.51051.6126-0.13596.1785-0.43022.66026.991226.6503-51.0196
101.6881-2.7038-2.69912.6533-3.8715.6334-0.12631.37790.1685-1.72640.01811.1567-3.42251.71650.56753.32880.5162-0.26133.53180.2432.911618.642614.4364-60.7216
113.5136-0.69310.69049.0547-5.45573.04841.79811.02440.61020.9673-1.9185-0.2385-2.49961.4170.32954.9520.7349-0.18393.73330.10522.913817.910335.661-31.2702
121.11712.5758-2.03657.9261-7.80158.4928.04267.991610.9267-8.88781.69770.09767.4484-8.4131-9.42034.54091.4128-0.3025.95090.65455.165514.32535.3121-46.3583
132.04542.6817-7.59370.5435-1.14532.9601-2.91896.5540.65210.08060.47-2.3601-0.1809-5.04920.5610.24221.73460.28874.8403-0.23681.71156.310340.8517-43.0763
149.662-2.59195.93894.47762.36299.8422-1.3937-0.0792.3942-3.54520.83752.8904-5.2847-0.60880.78164.3717-0.21720.0342.46450.54173.63915.357731.5883-24.4846
158.2262-4.23580.53273.1951.65522.4573-2.3709-1.34471.70012.60832.15450.5052-0.11410.77260.45785.6887-0.3127-0.04662.22960.04733.259944.326210.8159-63.3067
163.40394.316-3.48136.2395-4.75713.8948-1.65681.69931.4155-0.90990.05370.50236.55040.98562.00047.95241.14270.47753.60120.43533.375742.94019.7835-74.1966
177.5202-1.38231.96042.96820.26320.9394-0.3924-1.75570.0546-2.21440.71292.1357-2.12850.4259-0.39974.9821-0.08980.24843.75140.91113.247536.313812.7113-66.5211
186.08492.8401-4.11822.1326-3.14495.32991.75641.3647-0.15344.45441.5469-2.2277-1.30230.792-0.58194.6751-1.1060.37183.0534-0.02523.358461.2864-15.3796-3.4389
192.3294-1.8249-2.20692.37694.06494.29350.9645-0.89850.45321.3189-1.1131-1.2607-1.99241.11720.38432.5879-0.3245-0.82432.33890.24073.318761.796-23.12889.9258
206.7349-2.51794.76986.2769-2.30373.49472.54114.5527-3.4762-2.6806-3.03551.14674.35980.90530.77891.1147-2.7319-1.59740.5669-0.72634.21566.2845-28.9069-4.0306
211.90418.52297.50615.45414.14494.27521.6394-4.43888.37251.0548-1.3275.8094-3.8752-0.3104-1.37063.80310.28531.03711.64730.32426.034558.931-10.3785-42.7102
221.19451.53461.43624.5941-0.24079.5732-0.8793-0.5585-0.8306-1.61790.1115-0.51830.93450.34191.11682.7508-0.12960.4652.7580.27873.085870.6976-26.5954-43.0087
237.8811-5.8907-1.7565.14810.96413.28683.87161.05170.68210.0271-4.082-2.61391.6713-1.62140.07375.2038-0.62530.44072.9855-0.32953.739967.5229-19.5771-60.1171
248.7584-6.6328-1.81659.7251-3.71645.85361.60385.8827-14.28844.29523.97012.41853.58471.6569-1.67357.6206-1.4304-2.78684.5432-0.09137.348312.057211.571-21.3528
254.2925-2.2572-1.54845.91776.72238.8389-1.04530.81371.8007-0.5614-0.3001-0.4338-0.3253-2.27831.31663.57671.0855-0.14043.48580.32313.04514.47221.1237-7.9058
269.4784-0.52670.81686.23327.65888.96871.32571.26130.4001-2.3461-0.8139-0.3657-2.61720.495-0.83294.2312-0.4578-0.39672.7185-0.09073.079731.830315.75788.9603
275.6122-4.2895-0.91896.1871-2.38945.4708-1.78060.9918-0.32561.28490.66930.4342-0.1118-1.69342.37116.0273-0.08490.03992.7081-0.35572.923224.590518.14714.9065
285.83890.1808-1.8420.85682.50363.843-3.8372-1.11050.2723-1.63381.6987-1.0514-1.9565-1.4041.8375.59720.37460.69022.4830.11952.674835.08955.321217.5097
292.01075.20192.51754.4103-2.31838.2447-2.93321.33023.04117.01070.71198.2777-4.81352.34631.3599.3157-0.7974-0.04773.9352-0.03455.27744.56-20.6325-47.1614
305.3311-2.2506-2.42885.40211.58713.35940.6631-0.56231.08672.12170.07170.8424-2.07480.2161-0.19854.96180.6276-0.05272.7436-0.16932.485947.2851-19.0142-67.0397
313.4071-2.21620.24211.12870.71944.94183.59053.9644-2.82432.9945-3.9204-1.9025-1.4876-3.1954-1.17044.2264-0.15750.25184.4202-1.32114.184556.9542-31.7458-59.6999
324.11676.4448-4.23162.0034-5.6795.4375-0.4287.175-7.8043-5.34822.60180.3994.3945-2.4729-1.22335.3209-0.1954-1.53134.4104-0.9623.464427.2332-7.30761.0323
336.4641-6.44143.55278.5327-2.50930.6634-0.9335-1.0064-0.5367-1.28070.8454-0.4379-1.90380.118-0.18963.7010.08630.06093.2313-0.33352.257933.6866-13.764317.7967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid -3 through 38 )H0
2X-RAY DIFFRACTION2chain 'H' and (resid 39 through 84 )H0
3X-RAY DIFFRACTION3chain 'H' and (resid 85 through 98 )H0
4X-RAY DIFFRACTION4chain 'H' and (resid 99 through 148 )H0
5X-RAY DIFFRACTION5chain 'H' and (resid 149 through 165 )H0
6X-RAY DIFFRACTION6chain 'H' and (resid 166 through 174 )H0
7X-RAY DIFFRACTION7chain 'B' and (resid -1 through 26 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 76 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 85 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 171 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid -3 through 76 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 77 through 85 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 86 through 98 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 99 through 168 )C0
15X-RAY DIFFRACTION15chain 'A' and (resid -3 through 49 )A0
16X-RAY DIFFRACTION16chain 'A' and (resid 50 through 85 )A0
17X-RAY DIFFRACTION17chain 'A' and (resid 86 through 171 )A0
18X-RAY DIFFRACTION18chain 'G' and (resid -3 through 20 )G0
19X-RAY DIFFRACTION19chain 'G' and (resid 21 through 112 )G0
20X-RAY DIFFRACTION20chain 'G' and (resid 113 through 171 )G0
21X-RAY DIFFRACTION21chain 'I' and (resid -3 through 6 )I0
22X-RAY DIFFRACTION22chain 'I' and (resid 7 through 134 )I0
23X-RAY DIFFRACTION23chain 'I' and (resid 135 through 173 )I0
24X-RAY DIFFRACTION24chain 'D' and (resid -3 through 6 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 7 through 166 )D0
26X-RAY DIFFRACTION26chain 'E' and (resid -3 through 49 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 50 through 112 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 113 through 174 )E0
29X-RAY DIFFRACTION29chain 'J' and (resid -3 through 6 )J0
30X-RAY DIFFRACTION30chain 'J' and (resid 7 through 134 )J0
31X-RAY DIFFRACTION31chain 'J' and (resid 135 through 171 )J0
32X-RAY DIFFRACTION32chain 'F' and (resid -3 through 6 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 7 through 166 )F0

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