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- PDB-5dvb: Crystal Structure of S. cerevisiae TSA2 -

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Basic information

Entry
Database: PDB / ID: 5dvb
TitleCrystal Structure of S. cerevisiae TSA2
ComponentsTsa2p
KeywordsOXIDOREDUCTASE / Peroxiredoxin / Peroxidase / Oxidative Stress
Function / homology
Function and homology information


NFE2L2 regulating anti-oxidant/detoxification enzymes / TP53 Regulates Metabolic Genes / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / thioredoxin peroxidase 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 / peroxiredoxin activity / thioredoxin peroxidase 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Peroxiredoxin TSA2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNielsen, M.H. / Kidmose, R.T. / Jenner, L.B.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordic Foundation Denmark
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
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 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: Tsa2p
B: Tsa2p
C: Tsa2p
A: Tsa2p
G: Tsa2p
I: Tsa2p
D: Tsa2p
E: Tsa2p
J: Tsa2p
F: Tsa2p


Theoretical massNumber of molelcules
Total (without water)241,96510
Polymers241,96510
Non-polymers00
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19050 Å2
ΔGint-91 kcal/mol
Surface area72060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.530, 216.130, 64.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Tsa2p


Mass: 24196.477 Da / Num. of mol.: 10 / Mutation: C48S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TSA2, H834_YJM1574D00663 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D4RBH7, UniProt: Q04120*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.47 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 6% (v/v) Tacsimate pH 8 and 16% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→42.88 Å / Num. all: 122589 / Num. obs: 122589 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 124 % / Biso Wilson estimate: 52.27 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.166 / Χ2: 1.161 / Net I/σ(I): 33.67 / Num. measured all: 15148713
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.250.544.9611.11606497790379024.994100
2.25-2.30.8063.7021.78695642726872683.721100
2.3-2.50.9442.1093.77281611023428234282.118100
2.5-30.9960.66213.57469549934940349400.664100
3-410.16652.55373252927990279900.167100
4-510.09894.97126982710102101020.099100
5-1010.079100.41171545946594650.079100
10-2010.057112.14143773128012800.057100
20-2510.057109.611017696960.057100
25-3010.06298.06452247470.062100
30-400.9770.06283.93239337370.062100
400.9990.8545.6420033130.89139.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SBC

3sbc


Resolution: 2.2→45.716 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1907 1.63 %
Rwork0.1869 --
obs0.1877 117020 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13857 0 0 463 14320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01514182
X-RAY DIFFRACTIONf_angle_d1.43519222
X-RAY DIFFRACTIONf_dihedral_angle_d19.2518622
X-RAY DIFFRACTIONf_chiral_restr0.0642167
X-RAY DIFFRACTIONf_plane_restr0.0082464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.44071080.36256792X-RAY DIFFRACTION80
2.255-2.3160.30791240.2977245X-RAY DIFFRACTION85
2.316-2.38410.33071290.27267662X-RAY DIFFRACTION90
2.3841-2.46110.28261310.2567876X-RAY DIFFRACTION93
2.4611-2.5490.26831320.24028074X-RAY DIFFRACTION95
2.549-2.65110.26661390.22488335X-RAY DIFFRACTION97
2.6511-2.77170.26841390.23028365X-RAY DIFFRACTION98
2.7717-2.91780.29441400.23528483X-RAY DIFFRACTION99
2.9178-3.10060.28871420.22958558X-RAY DIFFRACTION100
3.1006-3.33990.27171430.21858590X-RAY DIFFRACTION100
3.3399-3.67590.26571410.19888619X-RAY DIFFRACTION100
3.6759-4.20750.22281440.16398694X-RAY DIFFRACTION100
4.2075-5.29970.18781450.13728742X-RAY DIFFRACTION100
5.2997-45.72620.17091500.15399078X-RAY DIFFRACTION100

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